diff --git a/Cargo.lock b/Cargo.lock
index 3077074e862fa..2303e74e52301 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -226,7 +226,7 @@ dependencies = [
  "bzip2",
  "crc",
  "flate2",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "liblzma",
  "rand 0.9.4",
  "serde",
@@ -356,7 +356,7 @@ dependencies = [
  "arrow-select",
  "chrono",
  "half",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "itoa",
  "lexical-core",
  "memchr",
@@ -511,7 +511,7 @@ checksum = "82f6aeea286b8eb4dd3431a1be1b59d290ace00f5bfd8e2a159bc2a05e2c1667"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 3.0.4",
+ "syn 3.0.3",
 ]
 
 [[package]]
@@ -1335,7 +1335,7 @@ dependencies = [
  "heck",
  "proc-macro2",
  "quote",
- "syn 3.0.4",
+ "syn 3.0.3",
 ]
 
 [[package]]
@@ -1510,9 +1510,9 @@ checksum = "217698eaf96b4a3f0bc4f3662aaa55bdf913cd54d7204591faa790070c6d0853"
 
 [[package]]
 name = "crc32fast"
-version = "1.5.1"
+version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8498c871161e1742aaa9d52551b2d6ebdd4c3d45a3be423e3728f33b955be550"
+checksum = "9481c1c90cbf2ac953f07c8d4a58aa3945c425b7185c9154d67a65e4230da511"
 dependencies = [
  "cfg-if",
 ]
@@ -1746,7 +1746,7 @@ dependencies = [
  "futures",
  "glob",
  "half",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "insta",
  "itertools 0.15.0",
  "liblzma",
@@ -1897,7 +1897,7 @@ dependencies = [
  "half",
  "hashbrown 0.17.1",
  "hex",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "insta",
  "itertools 0.15.0",
  "libc",
@@ -2173,7 +2173,7 @@ dependencies = [
  "datafusion-proto-common",
  "datafusion-proto-models",
  "env_logger",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "insta",
  "itertools 0.15.0",
  "recursive",
@@ -2187,7 +2187,7 @@ version = "55.0.0"
 dependencies = [
  "arrow",
  "datafusion-common",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "insta",
  "itertools 0.15.0",
  "rstest",
@@ -2367,7 +2367,7 @@ version = "55.0.0"
 dependencies = [
  "datafusion-doc",
  "quote",
- "syn 3.0.4",
+ "syn 3.0.3",
 ]
 
 [[package]]
@@ -2388,7 +2388,7 @@ dependencies = [
  "datafusion-physical-expr",
  "datafusion-sql",
  "env_logger",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "insta",
  "itertools 0.15.0",
  "log",
@@ -2413,7 +2413,7 @@ dependencies = [
  "datafusion-proto-models",
  "half",
  "hashbrown 0.17.1",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "insta",
  "itertools 0.15.0",
  "parking_lot",
@@ -2448,7 +2448,7 @@ dependencies = [
  "datafusion-expr-common",
  "datafusion-proto-models",
  "hashbrown 0.17.1",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "itertools 0.15.0",
  "parking_lot",
  "pin-project",
@@ -2506,7 +2506,7 @@ dependencies = [
  "futures",
  "half",
  "hashbrown 0.17.1",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "insta",
  "itertools 0.15.0",
  "log",
@@ -2565,7 +2565,7 @@ dependencies = [
  "arrow",
  "datafusion-common",
  "doc-comment",
- "pbjson 0.9.0",
+ "pbjson",
  "prost",
  "serde",
 ]
@@ -2576,7 +2576,7 @@ version = "55.0.0"
 dependencies = [
  "datafusion-common",
  "datafusion-proto-common",
- "pbjson 0.9.0",
+ "pbjson",
  "prost",
  "serde",
 ]
@@ -2659,7 +2659,7 @@ dependencies = [
  "datafusion-functions-nested",
  "datafusion-functions-window",
  "env_logger",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "insta",
  "itertools 0.15.0",
  "log",
@@ -3059,9 +3059,9 @@ dependencies = [
 
 [[package]]
 name = "flate2"
-version = "1.1.10"
+version = "1.1.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6e634e2e0ebac1ee034020da1ca582e17ffe4e0f5e985823721e168928136dcb"
+checksum = "843fba2746e448b37e26a819579957415c8cef339bf08564fe8b7ddbd959573c"
 dependencies = [
  "crc32fast",
  "miniz_oxide",
@@ -3208,7 +3208,7 @@ dependencies = [
 name = "gen"
 version = "0.1.0"
 dependencies = [
- "pbjson-build 0.9.0",
+ "pbjson-build",
  "prost-build",
 ]
 
@@ -3216,7 +3216,7 @@ dependencies = [
 name = "gen-common"
 version = "0.1.0"
 dependencies = [
- "pbjson-build 0.9.0",
+ "pbjson-build",
  "prost-build",
 ]
 
@@ -3302,7 +3302,7 @@ dependencies = [
  "futures-core",
  "futures-sink",
  "http 1.4.0",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "slab",
  "tokio",
  "tokio-util",
@@ -3721,6 +3721,26 @@ dependencies = [
  "icu_properties",
 ]
 
+[[package]]
+name = "include_dir"
+version = "0.7.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "923d117408f1e49d914f1a379a309cffe4f18c05cf4e3d12e613a15fc81bd0dd"
+dependencies = [
+ "glob",
+ "include_dir_macros",
+]
+
+[[package]]
+name = "include_dir_macros"
+version = "0.7.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7cab85a7ed0bd5f0e76d93846e0147172bed2e2d3f859bcc33a8d9699cad1a75"
+dependencies = [
+ "proc-macro2",
+ "quote",
+]
+
 [[package]]
 name = "indexmap"
 version = "1.9.3"
@@ -3734,9 +3754,9 @@ dependencies = [
 
 [[package]]
 name = "indexmap"
-version = "2.14.1"
+version = "2.14.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "07aa2048142242915a31d35844fb311e0e53fcca590c3a0a40dcf1b841fa09eb"
+checksum = "d466e9454f08e4a911e14806c24e16fba1b4c121d1ea474396f396069cf949d9"
 dependencies = [
  "equivalent",
  "hashbrown 0.17.1",
@@ -4072,9 +4092,9 @@ dependencies = [
 
 [[package]]
 name = "log"
-version = "0.4.34"
+version = "0.4.33"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f9f8bd3e56ce4dfc153cf470fffbfa98c7620958b312ca5c3a4b8d5181fd13c6"
+checksum = "0ceec5bc11778974d1bcb055b18002eba7f4b3518b6a0081b3af5f21666da9ad"
 
 [[package]]
 name = "lru-slab"
@@ -4150,9 +4170,9 @@ dependencies = [
 
 [[package]]
 name = "miniz_oxide"
-version = "0.9.1"
+version = "0.8.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b63fbc4a50860e98e7b2aa7804ded1db5cbc3aff9193adaff57a6931bf7c4b4c"
+checksum = "1fa76a2c86f704bdb222d66965fb3d63269ce38518b83cb0575fca855ebb6316"
 dependencies = [
  "adler2",
  "simd-adler32",
@@ -4562,16 +4582,6 @@ dependencies = [
  "syn 2.0.119",
 ]
 
-[[package]]
-name = "pbjson"
-version = "0.8.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "898bac3fa00d0ba57a4e8289837e965baa2dee8c3749f3b11d45a64b4223d9c3"
-dependencies = [
- "base64 0.22.1",
- "serde",
-]
-
 [[package]]
 name = "pbjson"
 version = "0.9.0"
@@ -4582,18 +4592,6 @@ dependencies = [
  "serde",
 ]
 
-[[package]]
-name = "pbjson-build"
-version = "0.8.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "af22d08a625a2213a78dbb0ffa253318c5c79ce3133d32d296655a7bdfb02095"
-dependencies = [
- "heck",
- "itertools 0.14.0",
- "prost",
- "prost-types",
-]
-
 [[package]]
 name = "pbjson-build"
 version = "0.9.0"
@@ -4608,14 +4606,14 @@ dependencies = [
 
 [[package]]
 name = "pbjson-types"
-version = "0.8.0"
+version = "0.9.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8e748e28374f10a330ee3bb9f29b828c0ac79831a32bab65015ad9b661ead526"
+checksum = "a14e2757d877c0f607a82ce1b8560e224370f159d66c5d52eb55ea187ef0350e"
 dependencies = [
  "bytes",
  "chrono",
- "pbjson 0.8.0",
- "pbjson-build 0.8.0",
+ "pbjson",
+ "pbjson-build",
  "prost",
  "prost-build",
  "serde",
@@ -4635,7 +4633,7 @@ checksum = "8701b58ea97060d5e5b155d383a69952a60943f0e6dfe30b04c287beb0b27455"
 dependencies = [
  "fixedbitset",
  "hashbrown 0.15.5",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "serde",
 ]
 
@@ -4850,6 +4848,16 @@ dependencies = [
  "syn 2.0.119",
 ]
 
+[[package]]
+name = "prettyplease"
+version = "0.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2bfe0f4c752e450fc2faf62654f1c134747922825d5b04ca717b8874f41a40c0"
+dependencies = [
+ "proc-macro2",
+ "syn 3.0.3",
+]
+
 [[package]]
 name = "proc-macro-crate"
 version = "3.5.0"
@@ -4889,7 +4897,7 @@ dependencies = [
  "log",
  "multimap",
  "petgraph",
- "prettyplease",
+ "prettyplease 0.2.37",
  "prost",
  "prost-types",
  "regex",
@@ -5246,9 +5254,9 @@ checksum = "d6f6ff9a378485b298a5286656da665ba74413d36db0979633275d2e708145d4"
 
 [[package]]
 name = "regress"
-version = "0.10.5"
+version = "0.11.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2057b2325e68a893284d1538021ab90279adac1139957ca2a74426c6f118fb48"
+checksum = "158a764437582235e3501f683b93a0a6f8d825d04a789dbe5ed30b8799b8908a"
 dependencies = [
  "hashbrown 0.16.1",
  "memchr",
@@ -5605,7 +5613,7 @@ checksum = "e7a5d71263a5a7d47b41f6b3f06ba276f10cc18b0931f1799f710578e2309348"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 3.0.4",
+ "syn 3.0.3",
 ]
 
 [[package]]
@@ -5625,7 +5633,7 @@ version = "1.0.151"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "c841b55ecdae098c80dcae9cf767f6f8a0c2cdb3416bbef72181df4d0fe73f14"
 dependencies = [
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "itoa",
  "memchr",
  "serde",
@@ -5688,7 +5696,7 @@ dependencies = [
  "chrono",
  "hex",
  "indexmap 1.9.3",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "schemars 0.9.0",
  "schemars 1.2.1",
  "serde_core",
@@ -5715,7 +5723,7 @@ version = "0.9.34+deprecated"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "6a8b1a1a2ebf674015cc02edccce75287f1a0130d394307b36743c2f5d504b47"
 dependencies = [
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "itoa",
  "ryu",
  "serde",
@@ -6035,28 +6043,55 @@ dependencies = [
 
 [[package]]
 name = "substrait"
-version = "0.63.0"
+version = "0.65.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "47f793c23baf7aa21919e0c2253ac3a47a306ced93359f036629a2d959dfe284"
+dependencies = [
+ "indexmap 2.14.0",
+ "prost",
+ "semver",
+ "serde",
+ "serde_json",
+ "substrait-extensions",
+ "substrait-prost",
+ "toml",
+]
+
+[[package]]
+name = "substrait-extensions"
+version = "0.102.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e620ff4d5c02fd6f7752931aa74b16a26af66a63022cc1ad412c77edbe0bab47"
+checksum = "d33afcbcf85005f788199c2de7983caef24d858c6909391208f8aad2516db46d"
 dependencies = [
  "heck",
- "indexmap 2.14.1",
- "pbjson 0.8.0",
- "pbjson-build 0.8.0",
+ "include_dir",
+ "indexmap 2.14.0",
+ "prettyplease 0.3.0",
+ "regress",
+ "schemars 0.8.22",
+ "serde",
+ "serde_json",
+ "serde_yaml",
+ "syn 3.0.3",
+ "typify",
+ "walkdir",
+]
+
+[[package]]
+name = "substrait-prost"
+version = "0.102.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ee6b74c488901400ff424a98b3505a105dd041de1aa9c355dad9f7f6115b4521"
+dependencies = [
+ "pbjson",
+ "pbjson-build",
  "pbjson-types",
- "prettyplease",
  "prost",
  "prost-build",
  "prost-types",
  "protobuf-src",
- "regress",
- "schemars 0.8.22",
- "semver",
  "serde",
  "serde_json",
- "serde_yaml",
- "syn 2.0.119",
- "typify",
  "walkdir",
 ]
 
@@ -6079,9 +6114,9 @@ dependencies = [
 
 [[package]]
 name = "syn"
-version = "3.0.4"
+version = "3.0.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e6275cddf4610d1775e6d1fe9469b2e77d0f39fd98fb7450901b821e0c53649f"
+checksum = "53e9bae58849f64dfa4f5d5ae372c8341f7305f82a3868709269343628b659a3"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -6204,7 +6239,7 @@ checksum = "bc04cd3e1236dd4a98afca4569f2deb3f120e5422a4023be2cb683f8486292af"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 3.0.4",
+ "syn 3.0.3",
 ]
 
 [[package]]
@@ -6387,7 +6422,7 @@ version = "1.1.4+spec-1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3aace63f4bbcdfc2c965b059de67119c89c4017a70d633be6c104910f67056f5"
 dependencies = [
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "serde_core",
  "serde_spanned",
  "toml_datetime",
@@ -6411,7 +6446,7 @@ version = "0.25.11+spec-1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0b59c4d22ed448339746c59b905d24568fcbb3ab65a500494f7b8c3e97739f2b"
 dependencies = [
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "toml_datetime",
  "toml_parser",
  "winnow",
@@ -6480,7 +6515,7 @@ checksum = "ebe5ef63511595f1344e2d5cfa636d973292adc0eec1f0ad45fae9f0851ab1d4"
 dependencies = [
  "futures-core",
  "futures-util",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "pin-project-lite",
  "slab",
  "sync_wrapper",
@@ -6586,9 +6621,9 @@ checksum = "e421abadd41a4225275504ea4d6566923418b7f05506fbc9c0fe86ba7396114b"
 
 [[package]]
 name = "twox-hash"
-version = "2.1.4"
+version = "2.1.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5283634e518fe9e82c7b20520bb4bc209009fd16c82077c802f8111ecbb0117a"
+checksum = "8464ec13c3691491391d9fce00f6416c9a48e46972f72d7865688be2080192c9"
 dependencies = [
  "rand 0.10.1",
 ]
@@ -6601,9 +6636,9 @@ checksum = "40ce102ab67701b8526c123c1bab5cbe42d7040ccfd0f64af1a385808d2f43de"
 
 [[package]]
 name = "typify"
-version = "0.5.0"
+version = "0.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e6d5bcc6f62eb1fa8aa4098f39b29f93dcb914e17158b76c50360911257aa629"
+checksum = "8cdc2e612ea322c6e232d46a0b34607c8eb28978fd6060ecfb139f2a50db8d5f"
 dependencies = [
  "typify-impl",
  "typify-macro",
@@ -6611,9 +6646,9 @@ dependencies = [
 
 [[package]]
 name = "typify-impl"
-version = "0.5.0"
+version = "0.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a1eb359f7ffa4f9ebe947fa11a1b2da054564502968db5f317b7e37693cb2240"
+checksum = "691591f49550c0d371bc441d019c30ce241d4116aee7d68df7a9840d6c70bf8f"
 dependencies = [
  "heck",
  "log",
@@ -6631,9 +6666,9 @@ dependencies = [
 
 [[package]]
 name = "typify-macro"
-version = "0.5.0"
+version = "0.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "911c32f3c8514b048c1b228361bebb5e6d73aeec01696e8cc0e82e2ffef8ab7a"
+checksum = "d41aea893c49cf95661389207b8af0c6254ff48b2c3ae1e4f3704777dbdfcf03"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -6781,9 +6816,9 @@ checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821"
 
 [[package]]
 name = "uuid"
-version = "1.26.0"
+version = "1.24.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b5772d71c9be8a8a6ac2117d949c5b224c1b72241bb611d9a3012edcf8af7812"
+checksum = "2cefc03fd367c0c6d4305de1b312cf00248c4114f4a0418ce6a6af769e3b0bd9"
 dependencies = [
  "getrandom 0.4.2",
  "js-sys",
@@ -6989,7 +7024,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "bb0e353e6a2fbdc176932bbaab493762eb1255a7900fe0fea1a2f96c296cc909"
 dependencies = [
  "anyhow",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "wasm-encoder",
  "wasmparser",
 ]
@@ -7015,7 +7050,7 @@ checksum = "47b807c72e1bac69382b3a6fb3dbe8ea4c0ed87ff5629b8685ae6b9a611028fe"
 dependencies = [
  "bitflags",
  "hashbrown 0.15.5",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "semver",
 ]
 
@@ -7392,8 +7427,8 @@ checksum = "b7c566e0f4b284dd6561c786d9cb0142da491f46a9fbed79ea69cdad5db17f21"
 dependencies = [
  "anyhow",
  "heck",
- "indexmap 2.14.1",
- "prettyplease",
+ "indexmap 2.14.0",
+ "prettyplease 0.2.37",
  "syn 2.0.119",
  "wasm-metadata",
  "wit-bindgen-core",
@@ -7407,7 +7442,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0c0f9bfd77e6a48eccf51359e3ae77140a7f50b1e2ebfe62422d8afdaffab17a"
 dependencies = [
  "anyhow",
- "prettyplease",
+ "prettyplease 0.2.37",
  "proc-macro2",
  "quote",
  "syn 2.0.119",
@@ -7423,7 +7458,7 @@ checksum = "9d66ea20e9553b30172b5e831994e35fbde2d165325bec84fc43dbf6f4eb9cb2"
 dependencies = [
  "anyhow",
  "bitflags",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "log",
  "serde",
  "serde_derive",
@@ -7442,7 +7477,7 @@ checksum = "ecc8ac4bc1dc3381b7f59c34f00b67e18f910c2c0f50015669dde7def656a736"
 dependencies = [
  "anyhow",
  "id-arena",
- "indexmap 2.14.1",
+ "indexmap 2.14.0",
  "log",
  "semver",
  "serde",
diff --git a/datafusion/substrait/Cargo.toml b/datafusion/substrait/Cargo.toml
index a0f203cec8db6..62aa8bdf573ea 100644
--- a/datafusion/substrait/Cargo.toml
+++ b/datafusion/substrait/Cargo.toml
@@ -42,9 +42,9 @@ half = { workspace = true }
 itertools = { workspace = true }
 object_store = { workspace = true }
 # We need to match the version in substrait, so we don't use the workspace version here
-pbjson-types = { version = "0.8.0" }
+pbjson-types = { version = "0.9.0" }
 prost = { workspace = true }
-substrait = { version = "0.63.0", features = ["serde"] }
+substrait = { version = "0.65.0", features = ["serde"] }
 url = { workspace = true }
 tokio = { workspace = true, features = ["fs"] }
 
diff --git a/datafusion/substrait/src/logical_plan/consumer/expr/field_reference.rs b/datafusion/substrait/src/logical_plan/consumer/expr/field_reference.rs
index be084f360358a..993c9ca91e4b5 100644
--- a/datafusion/substrait/src/logical_plan/consumer/expr/field_reference.rs
+++ b/datafusion/substrait/src/logical_plan/consumer/expr/field_reference.rs
@@ -74,7 +74,19 @@ fn resolve_outer_reference(
     outer_ref: &substrait::proto::expression::field_reference::OuterReference,
     field_idx: usize,
 ) -> datafusion::common::Result<Expr> {
-    let steps_out = outer_ref.steps_out as usize;
+    use substrait::proto::expression::field_reference::outer_reference::OuterReferenceType;
+    // `StepsOut` is deprecated in favour of `RelReference`, but a relation
+    // reference needs anchors that DataFusion does not assign.
+    #[expect(deprecated)]
+    let steps_out = match outer_ref.outer_reference_type {
+        Some(OuterReferenceType::StepsOut(steps_out)) => steps_out as usize,
+        Some(OuterReferenceType::RelReference(_)) => {
+            return not_impl_err!(
+                "OuterReference by relation reference is not supported"
+            );
+        }
+        None => return substrait_err!("OuterReference without a reference type"),
+    };
     let Some(outer_schema) = consumer.get_outer_schema(steps_out) else {
         return substrait_err!(
             "OuterReference with steps_out={steps_out} \
diff --git a/datafusion/substrait/src/logical_plan/consumer/expr/literal.rs b/datafusion/substrait/src/logical_plan/consumer/expr/literal.rs
index d7d7a69581f05..3222aef521309 100644
--- a/datafusion/substrait/src/logical_plan/consumer/expr/literal.rs
+++ b/datafusion/substrait/src/logical_plan/consumer/expr/literal.rs
@@ -25,9 +25,7 @@ use crate::variation_const::{
     INTERVAL_DAY_TIME_TYPE_REF, INTERVAL_MONTH_DAY_NANO_TYPE_NAME,
     INTERVAL_MONTH_DAY_NANO_TYPE_REF, INTERVAL_YEAR_MONTH_TYPE_REF,
     LARGE_CONTAINER_TYPE_VARIATION_REF, TIME_32_TYPE_VARIATION_REF,
-    TIME_64_TYPE_VARIATION_REF, TIMESTAMP_MICRO_TYPE_VARIATION_REF,
-    TIMESTAMP_MILLI_TYPE_VARIATION_REF, TIMESTAMP_NANO_TYPE_VARIATION_REF,
-    TIMESTAMP_SECOND_TYPE_VARIATION_REF, UNSIGNED_INTEGER_TYPE_VARIATION_REF,
+    TIME_64_TYPE_VARIATION_REF, UNSIGNED_INTEGER_TYPE_VARIATION_REF,
     VIEW_CONTAINER_TYPE_VARIATION_REF,
 };
 use datafusion::arrow::array::{AsArray, MapArray, new_empty_array};
@@ -46,7 +44,6 @@ use substrait::proto::expression::Literal;
 use substrait::proto::expression::literal::user_defined::{TypeAnchorType, Val};
 use substrait::proto::expression::literal::{
     IntervalCompound, IntervalDayToSecond, IntervalYearToMonth, LiteralType,
-    interval_day_to_second,
 };
 
 pub async fn from_literal(
@@ -102,28 +99,6 @@ pub(crate) fn from_substrait_literal(
         },
         Some(LiteralType::Fp32(f)) => ScalarValue::Float32(Some(*f)),
         Some(LiteralType::Fp64(f)) => ScalarValue::Float64(Some(*f)),
-        #[expect(deprecated)]
-        Some(LiteralType::Timestamp(t)) => {
-            // Kept for backwards compatibility, new plans should use PrecisionTimestamp(Tz) instead
-            #[expect(deprecated)]
-            match lit.type_variation_reference {
-                TIMESTAMP_SECOND_TYPE_VARIATION_REF => {
-                    ScalarValue::TimestampSecond(Some(*t), None)
-                }
-                TIMESTAMP_MILLI_TYPE_VARIATION_REF => {
-                    ScalarValue::TimestampMillisecond(Some(*t), None)
-                }
-                TIMESTAMP_MICRO_TYPE_VARIATION_REF => {
-                    ScalarValue::TimestampMicrosecond(Some(*t), None)
-                }
-                TIMESTAMP_NANO_TYPE_VARIATION_REF => {
-                    ScalarValue::TimestampNanosecond(Some(*t), None)
-                }
-                others => {
-                    return substrait_err!("Unknown type variation reference {others}");
-                }
-            }
-        }
         Some(LiteralType::PrecisionTimestamp(pt)) => match pt.precision {
             0 => ScalarValue::TimestampSecond(Some(pt.value), None),
             3 => ScalarValue::TimestampMillisecond(Some(pt.value), None),
@@ -381,29 +356,17 @@ pub(crate) fn from_substrait_literal(
             days,
             seconds,
             subseconds,
-            precision_mode,
+            precision,
         })) => {
-            use interval_day_to_second::PrecisionMode;
             // DF only supports millisecond precision, so for any more granular type we lose precision
-            let milliseconds = match precision_mode {
-                #[expect(deprecated)]
-                Some(PrecisionMode::Microseconds(ms)) => ms / 1000,
-                None => {
-                    if *subseconds != 0 {
-                        return substrait_err!(
-                            "Cannot set subseconds field of IntervalDayToSecond without setting precision"
-                        );
-                    } else {
-                        0_i32
-                    }
-                }
-                Some(PrecisionMode::Precision(0)) => *subseconds as i32 * 1000,
-                Some(PrecisionMode::Precision(3)) => *subseconds as i32,
-                Some(PrecisionMode::Precision(6)) => (subseconds / 1000) as i32,
-                Some(PrecisionMode::Precision(9)) => (subseconds / 1000 / 1000) as i32,
-                _ => {
+            let milliseconds = match precision {
+                0 => *subseconds as i32 * 1000,
+                3 => *subseconds as i32,
+                6 => (subseconds / 1000) as i32,
+                9 => (subseconds / 1000 / 1000) as i32,
+                p => {
                     return not_impl_err!(
-                        "Unsupported Substrait interval day to second precision mode: {precision_mode:?}"
+                        "Unsupported Substrait interval day to second precision: {p}"
                     );
                 }
             };
@@ -423,8 +386,7 @@ pub(crate) fn from_substrait_literal(
                     days,
                     seconds,
                     subseconds,
-                    precision_mode:
-                        Some(interval_day_to_second::PrecisionMode::Precision(p)),
+                    precision: p,
                 }),
             ) => {
                 if *p < 0 || *p > 9 {
@@ -607,9 +569,7 @@ mod tests {
                     days: 3,
                     seconds: 4,
                     subseconds: 5,
-                    precision_mode: Some(
-                        interval_day_to_second::PrecisionMode::Precision(6),
-                    ),
+                    precision: 6,
                 }),
             })),
         };
diff --git a/datafusion/substrait/src/logical_plan/consumer/expr/mod.rs b/datafusion/substrait/src/logical_plan/consumer/expr/mod.rs
index 623bb715cd838..5b8ca8396f114 100644
--- a/datafusion/substrait/src/logical_plan/consumer/expr/mod.rs
+++ b/datafusion/substrait/src/logical_plan/consumer/expr/mod.rs
@@ -62,6 +62,9 @@ pub async fn from_substrait_rex(
 ) -> datafusion::common::Result<Expr> {
     match &expression.rex_type {
         Some(t) => match t {
+            RexType::ExecutionContextVariable(_) => {
+                not_impl_err!("Execution context variables are not supported")
+            }
             RexType::Literal(expr) => consumer.consume_literal(expr).await,
             RexType::Selection(expr) => {
                 consumer.consume_field_reference(expr, input_schema).await
@@ -92,8 +95,6 @@ pub async fn from_substrait_rex(
                 consumer.consume_subquery(expr.as_ref(), input_schema).await
             }
             RexType::Nested(expr) => consumer.consume_nested(expr, input_schema).await,
-            #[expect(deprecated)]
-            RexType::Enum(expr) => consumer.consume_enum(expr, input_schema).await,
             RexType::DynamicParameter(expr) => {
                 consumer.consume_dynamic_parameter(expr, input_schema).await
             }
@@ -216,14 +217,14 @@ mod tests {
     async fn window_function_with_range_unit_and_no_order_by()
     -> datafusion::common::Result<()> {
         let substrait = Expression {
-            rex_type: Some(RexType::WindowFunction(
+            rex_type: Some(RexType::WindowFunction(Box::new(
                 substrait::proto::expression::WindowFunction {
                     function_reference: 0,
                     bounds_type: BoundsType::Range as i32,
                     sorts: vec![],
                     ..Default::default()
                 },
-            )),
+            ))),
         };
 
         let mut consumer = test_consumer();
@@ -247,12 +248,12 @@ mod tests {
     #[tokio::test]
     async fn window_function_with_count() -> datafusion::common::Result<()> {
         let substrait = Expression {
-            rex_type: Some(RexType::WindowFunction(
+            rex_type: Some(RexType::WindowFunction(Box::new(
                 substrait::proto::expression::WindowFunction {
                     function_reference: 0,
                     ..Default::default()
                 },
-            )),
+            ))),
         };
 
         let mut consumer = test_consumer();
@@ -274,13 +275,13 @@ mod tests {
     #[tokio::test]
     async fn window_function_with_invalid_invocation() {
         let substrait = Expression {
-            rex_type: Some(RexType::WindowFunction(
+            rex_type: Some(RexType::WindowFunction(Box::new(
                 substrait::proto::expression::WindowFunction {
                     function_reference: 0,
                     invocation: 3,
                     ..Default::default()
                 },
-            )),
+            ))),
         };
 
         let mut consumer = test_consumer();
diff --git a/datafusion/substrait/src/logical_plan/consumer/expr/window_function.rs b/datafusion/substrait/src/logical_plan/consumer/expr/window_function.rs
index d39b325a54827..b0cbcbf7c4128 100644
--- a/datafusion/substrait/src/logical_plan/consumer/expr/window_function.rs
+++ b/datafusion/substrait/src/logical_plan/consumer/expr/window_function.rs
@@ -27,11 +27,14 @@ use datafusion::logical_expr::expr::WindowFunctionParams;
 use datafusion::logical_expr::{
     Expr, WindowFrameBound, WindowFrameUnits, WindowFunctionDefinition, expr,
 };
+use substrait::proto::Expression;
 use substrait::proto::aggregate_function::AggregationInvocation;
 use substrait::proto::expression::WindowFunction;
+use substrait::proto::expression::literal::LiteralType;
 use substrait::proto::expression::window_function::{Bound, BoundsType};
 use substrait::proto::expression::{
-    window_function::bound as SubstraitBound, window_function::bound::Kind as BoundKind,
+    Literal, RexType, window_function::bound as SubstraitBound,
+    window_function::bound::Kind as BoundKind,
 };
 
 pub async fn from_window_function(
@@ -85,8 +88,8 @@ pub async fn from_window_function(
     };
     let window_frame = datafusion::logical_expr::WindowFrame::new_bounds(
         bound_units,
-        from_substrait_bound(window.lower_bound.as_ref(), true)?,
-        from_substrait_bound(window.upper_bound.as_ref(), false)?,
+        from_substrait_bound(window.lower_bound.as_deref(), true)?,
+        from_substrait_bound(window.upper_bound.as_deref(), false)?,
     );
 
     window_frame.regularize_order_bys(&mut order_by)?;
@@ -139,20 +142,32 @@ fn from_substrait_bound(
                 BoundKind::CurrentRow(SubstraitBound::CurrentRow {}) => {
                     Ok(WindowFrameBound::CurrentRow)
                 }
-                BoundKind::Preceding(SubstraitBound::Preceding { offset }) => {
-                    if *offset <= 0 {
+                BoundKind::Preceding(bound) => {
+                    #[expect(deprecated)]
+                    let offset =
+                        bound_offset(bound.offset, bound.offset_expr.as_deref())?;
+                    let Some(offset) = offset else {
+                        return Ok(WindowFrameBound::CurrentRow);
+                    };
+                    if offset <= 0 {
                         return plan_err!("Preceding bound must be positive");
                     }
                     Ok(WindowFrameBound::Preceding(ScalarValue::UInt64(Some(
-                        *offset as u64,
+                        offset as u64,
                     ))))
                 }
-                BoundKind::Following(SubstraitBound::Following { offset }) => {
-                    if *offset <= 0 {
+                BoundKind::Following(bound) => {
+                    #[expect(deprecated)]
+                    let offset =
+                        bound_offset(bound.offset, bound.offset_expr.as_deref())?;
+                    let Some(offset) = offset else {
+                        return Ok(WindowFrameBound::CurrentRow);
+                    };
+                    if offset <= 0 {
                         return plan_err!("Following bound must be positive");
                     }
                     Ok(WindowFrameBound::Following(ScalarValue::UInt64(Some(
-                        *offset as u64,
+                        offset as u64,
                     ))))
                 }
                 BoundKind::Unbounded(SubstraitBound::Unbounded {}) => {
@@ -174,3 +189,76 @@ fn from_substrait_bound(
         }
     }
 }
+
+/// Reads the distance of a window frame bound.
+///
+/// The specification requires a consumer to use `offset_expr` when it is set and
+/// to ignore `offset`, and defines a zero `offset_expr` as equivalent to
+/// CurrentRow, which `None` reports here. DataFusion frame bounds hold a
+/// literal, so an expression that is not an int64 literal cannot be
+/// represented.
+fn bound_offset(
+    offset: i64,
+    offset_expr: Option<&Expression>,
+) -> datafusion::common::Result<Option<i64>> {
+    match offset_expr {
+        Some(Expression {
+            rex_type:
+                Some(RexType::Literal(Literal {
+                    literal_type: Some(LiteralType::I64(value)),
+                    ..
+                })),
+        }) => Ok((*value != 0).then_some(*value)),
+        Some(_) => not_impl_err!(
+            "Window frame bound offsets other than int64 literals are not supported"
+        ),
+        None => Ok(Some(offset)),
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    fn i64_literal(value: i64) -> Expression {
+        Expression {
+            rex_type: Some(RexType::Literal(Literal {
+                literal_type: Some(LiteralType::I64(value)),
+                ..Default::default()
+            })),
+        }
+    }
+
+    /// A zero `offset_expr` is defined as equivalent to CurrentRow, so it is
+    /// read as such rather than rejected as a non-positive distance.
+    #[test]
+    fn zero_offset_expression_reads_as_current_row() {
+        #[expect(deprecated)]
+        let bound = Bound {
+            kind: Some(BoundKind::Preceding(Box::new(SubstraitBound::Preceding {
+                offset: 0,
+                offset_expr: Some(Box::new(i64_literal(0))),
+            }))),
+        };
+        assert_eq!(
+            from_substrait_bound(Some(&bound), true).unwrap(),
+            WindowFrameBound::CurrentRow
+        );
+    }
+
+    /// When `offset_expr` is set the consumer must use it and ignore `offset`.
+    #[test]
+    fn offset_expression_wins_over_the_deprecated_offset() {
+        #[expect(deprecated)]
+        let bound = Bound {
+            kind: Some(BoundKind::Preceding(Box::new(SubstraitBound::Preceding {
+                offset: 7,
+                offset_expr: Some(Box::new(i64_literal(3))),
+            }))),
+        };
+        assert_eq!(
+            from_substrait_bound(Some(&bound), true).unwrap(),
+            WindowFrameBound::Preceding(ScalarValue::UInt64(Some(3)))
+        );
+    }
+}
diff --git a/datafusion/substrait/src/logical_plan/consumer/rel/aggregate_rel.rs b/datafusion/substrait/src/logical_plan/consumer/rel/aggregate_rel.rs
index 8c0114b90ee13..acb08d3afb129 100644
--- a/datafusion/substrait/src/logical_plan/consumer/rel/aggregate_rel.rs
+++ b/datafusion/substrait/src/logical_plan/consumer/rel/aggregate_rel.rs
@@ -17,7 +17,7 @@
 
 use crate::logical_plan::consumer::{NameTracker, SubstraitConsumer};
 use crate::logical_plan::consumer::{from_substrait_agg_func, from_substrait_sorts};
-use datafusion::common::{DFSchemaRef, not_impl_err};
+use datafusion::common::{not_impl_err, substrait_datafusion_err};
 use datafusion::logical_expr::{Expr, GroupingSet, LogicalPlan, LogicalPlanBuilder};
 use substrait::proto::AggregateRel;
 use substrait::proto::aggregate_function::AggregationInvocation;
@@ -42,26 +42,16 @@ pub async fn from_aggregate_rel(
         match agg.groupings.len() {
             0 => {}
             1 => {
-                group_exprs.extend_from_slice(
-                    &from_substrait_grouping(
-                        consumer,
-                        &agg.groupings[0],
-                        &ref_group_exprs,
-                        input.schema(),
-                    )
-                    .await?,
-                );
+                group_exprs.extend_from_slice(&from_substrait_grouping(
+                    &agg.groupings[0],
+                    &ref_group_exprs,
+                )?);
             }
             _ => {
                 let mut grouping_sets = vec![];
                 for grouping in &agg.groupings {
-                    let grouping_set = from_substrait_grouping(
-                        consumer,
-                        grouping,
-                        &ref_group_exprs,
-                        input.schema(),
-                    )
-                    .await?;
+                    let grouping_set =
+                        from_substrait_grouping(grouping, &ref_group_exprs)?;
                     grouping_sets.push(grouping_set);
                 }
                 // Single-element grouping expression of type Expr::GroupingSet.
@@ -128,24 +118,22 @@ pub async fn from_aggregate_rel(
     }
 }
 
-#[expect(deprecated)]
-async fn from_substrait_grouping(
-    consumer: &impl SubstraitConsumer,
+/// A grouping set names the expressions it groups by index into the
+/// relation-level `grouping_expressions`.
+fn from_substrait_grouping(
     grouping: &Grouping,
     expressions: &[Expr],
-    input_schema: &DFSchemaRef,
 ) -> datafusion::common::Result<Vec<Expr>> {
-    let mut group_exprs = vec![];
-    if !grouping.grouping_expressions.is_empty() {
-        for e in &grouping.grouping_expressions {
-            let expr = consumer.consume_expression(e, input_schema).await?;
-            group_exprs.push(expr);
-        }
-        return Ok(group_exprs);
-    }
-    for idx in &grouping.expression_references {
-        let e = &expressions[*idx as usize];
-        group_exprs.push(e.clone());
-    }
-    Ok(group_exprs)
+    grouping
+        .expression_references
+        .iter()
+        .map(|idx| {
+            expressions.get(*idx as usize).cloned().ok_or_else(|| {
+                substrait_datafusion_err!(
+                    "Grouping references expression {idx} but the aggregate declares {}",
+                    expressions.len()
+                )
+            })
+        })
+        .collect()
 }
diff --git a/datafusion/substrait/src/logical_plan/consumer/rel/fetch_rel.rs b/datafusion/substrait/src/logical_plan/consumer/rel/fetch_rel.rs
index 12a8a77199b1a..6f96d5b9d307f 100644
--- a/datafusion/substrait/src/logical_plan/consumer/rel/fetch_rel.rs
+++ b/datafusion/substrait/src/logical_plan/consumer/rel/fetch_rel.rs
@@ -18,8 +18,8 @@
 use crate::logical_plan::consumer::SubstraitConsumer;
 use async_recursion::async_recursion;
 use datafusion::common::{DFSchema, DFSchemaRef, not_impl_err};
-use datafusion::logical_expr::{LogicalPlan, LogicalPlanBuilder, lit};
-use substrait::proto::{FetchRel, fetch_rel};
+use datafusion::logical_expr::{LogicalPlan, LogicalPlanBuilder};
+use substrait::proto::FetchRel;
 
 #[async_recursion]
 pub async fn from_fetch_rel(
@@ -29,23 +29,14 @@ pub async fn from_fetch_rel(
     if let Some(input) = fetch.input.as_ref() {
         let input = LogicalPlanBuilder::from(consumer.consume_rel(input).await?);
         let empty_schema = DFSchemaRef::new(DFSchema::empty());
-        let offset = match &fetch.offset_mode {
-            #[expect(deprecated)]
-            Some(fetch_rel::OffsetMode::Offset(offset)) => Some(lit(*offset)),
-            Some(fetch_rel::OffsetMode::OffsetExpr(expr)) => {
-                Some(consumer.consume_expression(expr, &empty_schema).await?)
-            }
+        // Unset offset is treated as 0 and unset count signals that ALL records
+        // should be returned, so an absent expression maps to None either way.
+        let offset = match &fetch.offset_expr {
+            Some(expr) => Some(consumer.consume_expression(expr, &empty_schema).await?),
             None => None,
         };
-        let count = match &fetch.count_mode {
-            #[expect(deprecated)]
-            Some(fetch_rel::CountMode::Count(count)) => {
-                // -1 means that ALL records should be returned, equivalent to None
-                (*count != -1).then(|| lit(*count))
-            }
-            Some(fetch_rel::CountMode::CountExpr(expr)) => {
-                Some(consumer.consume_expression(expr, &empty_schema).await?)
-            }
+        let count = match &fetch.count_expr {
+            Some(expr) => Some(consumer.consume_expression(expr, &empty_schema).await?),
             None => None,
         };
         input.limit_by_expr(offset, count)?.build()
diff --git a/datafusion/substrait/src/logical_plan/consumer/rel/mod.rs b/datafusion/substrait/src/logical_plan/consumer/rel/mod.rs
index 038ada115b9d8..ec82fbc642d92 100644
--- a/datafusion/substrait/src/logical_plan/consumer/rel/mod.rs
+++ b/datafusion/substrait/src/logical_plan/consumer/rel/mod.rs
@@ -134,6 +134,8 @@ fn retrieve_rel_common(rel: &Rel) -> Option<&RelCommon> {
     match rel.rel_type.as_ref() {
         None => None,
         Some(rt) => match rt {
+            RelType::LateralJoin(l) => l.common.as_ref(),
+            RelType::TopN(t) => t.common.as_ref(),
             RelType::Read(r) => r.common.as_ref(),
             RelType::Filter(f) => f.common.as_ref(),
             RelType::Fetch(f) => f.common.as_ref(),
@@ -155,7 +157,7 @@ fn retrieve_rel_common(rel: &Rel) -> Option<&RelCommon> {
             RelType::Window(w) => w.common.as_ref(),
             RelType::Exchange(e) => e.common.as_ref(),
             RelType::Expand(e) => e.common.as_ref(),
-            RelType::Update(_) => None,
+            RelType::Update(u) => u.common.as_ref(),
         },
     }
 }
diff --git a/datafusion/substrait/src/logical_plan/consumer/rel/read_rel.rs b/datafusion/substrait/src/logical_plan/consumer/rel/read_rel.rs
index 2cad1440807a5..9457c155ed9e4 100644
--- a/datafusion/substrait/src/logical_plan/consumer/rel/read_rel.rs
+++ b/datafusion/substrait/src/logical_plan/consumer/rel/read_rel.rs
@@ -35,7 +35,6 @@ use substrait::proto::read_rel::local_files::file_or_files::PathType::UriFile;
 use substrait::proto::{Expression, ReadRel};
 use url::Url;
 
-#[expect(deprecated)]
 pub async fn from_read_rel(
     consumer: &impl SubstraitConsumer,
     read: &ReadRel,
@@ -114,14 +113,13 @@ pub async fn from_read_rel(
             .await
         }
         Some(ReadType::VirtualTable(vt)) => {
-            if vt.values.is_empty() && vt.expressions.is_empty() {
+            if vt.expressions.is_empty() {
                 return Ok(LogicalPlan::EmptyRelation(EmptyRelation {
                     produce_one_row: false,
                     schema: DFSchemaRef::new(substrait_schema),
                 }));
             }
 
-            // Check for produce_one_row pattern in both old (values) and new (expressions) formats.
             // A VirtualTable with exactly one row containing only empty/default fields represents
             // an EmptyRelation with produce_one_row=true. This pattern is used for queries without
             // a FROM clause (e.g., "SELECT 1 AS one") where a single phantom row is needed to
@@ -129,14 +127,9 @@ pub async fn from_read_rel(
             // the SQL "DUAL" table (see: https://en.wikipedia.org/wiki/DUAL_table) which some
             // databases provide as a single-row source for selecting constant expressions when no
             // real table is present.
-            let is_produce_one_row = (vt.values.len() == 1
-                && vt.expressions.is_empty()
+            let is_produce_one_row = vt.expressions.len() == 1
                 && substrait_schema.fields().is_empty()
-                && vt.values[0].fields.is_empty())
-                || (vt.expressions.len() == 1
-                    && vt.values.is_empty()
-                    && substrait_schema.fields().is_empty()
-                    && vt.expressions[0].fields.is_empty());
+                && vt.expressions[0].fields.is_empty();
 
             if is_produce_one_row {
                 return Ok(LogicalPlan::EmptyRelation(EmptyRelation {
@@ -145,7 +138,7 @@ pub async fn from_read_rel(
                 }));
             }
 
-            let values = if !vt.expressions.is_empty() {
+            let values = {
                 let mut exprs = vec![];
                 for row in &vt.expressions {
                     if row.fields.len() != substrait_schema.fields().len() {
@@ -195,8 +188,6 @@ pub async fn from_read_rel(
                     exprs.push(row_exprs);
                 }
                 exprs
-            } else {
-                convert_literal_rows(consumer, vt, named_struct)?
             };
 
             Ok(LogicalPlan::Values(Values {
@@ -251,46 +242,6 @@ pub async fn from_read_rel(
     }
 }
 
-/// Converts Substrait literal rows from a VirtualTable into DataFusion expressions.
-///
-/// This function processes the deprecated `values` field of VirtualTable, converting
-/// each literal value into a `Expr::Literal` while tracking and validating the name
-/// indices against the provided named struct schema.
-fn convert_literal_rows(
-    consumer: &impl SubstraitConsumer,
-    vt: &substrait::proto::read_rel::VirtualTable,
-    named_struct: &substrait::proto::NamedStruct,
-) -> datafusion::common::Result<Vec<Vec<Expr>>> {
-    #[expect(deprecated)]
-    vt.values
-        .iter()
-        .map(|row| {
-            let mut name_idx = 0;
-            let lits = row
-                .fields
-                .iter()
-                .map(|lit| {
-                    name_idx += 1; // top-level names are provided through schema
-                    Ok(Expr::Literal(from_substrait_literal(
-                        consumer,
-                        lit,
-                        &named_struct.names,
-                        &mut name_idx,
-                    )?, None))
-                })
-                .collect::<datafusion::common::Result<_>>()?;
-            if name_idx != named_struct.names.len() {
-                return substrait_err!(
-                    "Names list must match exactly to nested schema, but found {} uses for {} names",
-                    name_idx,
-                    named_struct.names.len()
-                );
-            }
-            Ok(lits)
-        })
-        .collect::<datafusion::common::Result<_>>()
-}
-
 pub fn apply_masking(
     schema: DFSchema,
     mask_expression: Option<&MaskExpression>,
diff --git a/datafusion/substrait/src/logical_plan/consumer/substrait_consumer.rs b/datafusion/substrait/src/logical_plan/consumer/substrait_consumer.rs
index bbd80b4cff001..4de2a4503024e 100644
--- a/datafusion/substrait/src/logical_plan/consumer/substrait_consumer.rs
+++ b/datafusion/substrait/src/logical_plan/consumer/substrait_consumer.rs
@@ -40,8 +40,8 @@ use std::collections::VecDeque;
 use std::sync::{Arc, RwLock};
 use substrait::proto::expression as substrait_expression;
 use substrait::proto::expression::{
-    Enum, FieldReference, IfThen, Literal, MultiOrList, Nested, ScalarFunction,
-    SingularOrList, SwitchExpression, WindowFunction,
+    FieldReference, IfThen, Literal, MultiOrList, Nested, ScalarFunction, SingularOrList,
+    SwitchExpression, WindowFunction,
 };
 use substrait::proto::{self, Type};
 use substrait::proto::{
@@ -388,14 +388,6 @@ pub trait SubstraitConsumer: Send + Sync + Sized {
         from_nested(self, expr, input_schema).await
     }
 
-    async fn consume_enum(
-        &self,
-        _expr: &Enum,
-        _input_schema: &DFSchema,
-    ) -> datafusion::common::Result<Expr> {
-        not_impl_err!("Enum expression not supported")
-    }
-
     async fn consume_dynamic_parameter(
         &self,
         expr: &DynamicParameter,
diff --git a/datafusion/substrait/src/logical_plan/consumer/types.rs b/datafusion/substrait/src/logical_plan/consumer/types.rs
index 6ca9ced2fcb06..c8e35ec12b965 100644
--- a/datafusion/substrait/src/logical_plan/consumer/types.rs
+++ b/datafusion/substrait/src/logical_plan/consumer/types.rs
@@ -27,14 +27,12 @@ use crate::variation_const::{
     INTERVAL_DAY_TIME_TYPE_REF, INTERVAL_MONTH_DAY_NANO_TYPE_NAME,
     INTERVAL_MONTH_DAY_NANO_TYPE_REF, INTERVAL_YEAR_MONTH_TYPE_REF,
     LARGE_CONTAINER_TYPE_VARIATION_REF, TIME_32_TYPE_VARIATION_REF,
-    TIME_64_TYPE_VARIATION_REF, TIMESTAMP_MICRO_TYPE_VARIATION_REF,
-    TIMESTAMP_MILLI_TYPE_VARIATION_REF, TIMESTAMP_NANO_TYPE_VARIATION_REF,
-    TIMESTAMP_SECOND_TYPE_VARIATION_REF, UNSIGNED_INTEGER_TYPE_VARIATION_REF,
+    TIME_64_TYPE_VARIATION_REF, UNSIGNED_INTEGER_TYPE_VARIATION_REF,
     VIEW_CONTAINER_TYPE_VARIATION_REF,
 };
 use crate::variation_const::{FLOAT_16_TYPE_NAME, NULL_TYPE_NAME};
 use datafusion::arrow::datatypes::{
-    DataType, Field, FieldRef, Fields, IntervalUnit, Schema, TimeUnit,
+    DataType, Field, FieldRef, Fields, IntervalUnit, Schema,
 };
 use datafusion::common::datatype::DataTypeExt;
 use datafusion::common::{
@@ -106,28 +104,6 @@ pub fn from_substrait_type(
             },
             r#type::Kind::Fp32(_) => Ok(DataType::Float32),
             r#type::Kind::Fp64(_) => Ok(DataType::Float64),
-            #[expect(deprecated)]
-            r#type::Kind::Timestamp(ts) => {
-                // Kept for backwards compatibility, new plans should use PrecisionTimestamp(Tz) instead
-                #[expect(deprecated)]
-                match ts.type_variation_reference {
-                    TIMESTAMP_SECOND_TYPE_VARIATION_REF => {
-                        Ok(DataType::Timestamp(TimeUnit::Second, None))
-                    }
-                    TIMESTAMP_MILLI_TYPE_VARIATION_REF => {
-                        Ok(DataType::Timestamp(TimeUnit::Millisecond, None))
-                    }
-                    TIMESTAMP_MICRO_TYPE_VARIATION_REF => {
-                        Ok(DataType::Timestamp(TimeUnit::Microsecond, None))
-                    }
-                    TIMESTAMP_NANO_TYPE_VARIATION_REF => {
-                        Ok(DataType::Timestamp(TimeUnit::Nanosecond, None))
-                    }
-                    v => not_impl_err!(
-                        "Unsupported Substrait type variation {v} of type {s_kind:?}"
-                    ),
-                }
-            }
             r#type::Kind::PrecisionTimestamp(pts) => {
                 let unit = from_substrait_precision(pts.precision, "PrecisionTimestamp")?;
                 Ok(DataType::Timestamp(unit, None))
@@ -368,13 +344,7 @@ fn type_is_nullable(dt: &Type) -> datafusion::common::Result<bool> {
         r#type::Kind::I64(integer) => integer.nullability,
         r#type::Kind::Fp32(float) => float.nullability,
         r#type::Kind::Fp64(float) => float.nullability,
-        #[expect(deprecated)]
-        r#type::Kind::Timestamp(timestamp) => timestamp.nullability,
         r#type::Kind::Date(date) => date.nullability,
-        #[expect(deprecated)]
-        r#type::Kind::Time(time) => time.nullability,
-        #[expect(deprecated)]
-        r#type::Kind::TimestampTz(timestamp) => timestamp.nullability,
         r#type::Kind::IntervalYear(interval) => interval.nullability,
         r#type::Kind::IntervalDay(interval) => interval.nullability,
         r#type::Kind::IntervalCompound(interval) => interval.nullability,
@@ -393,8 +363,7 @@ fn type_is_nullable(dt: &Type) -> datafusion::common::Result<bool> {
         r#type::Kind::Map(map) => map.nullability,
         r#type::Kind::Func(func) => func.nullability,
         r#type::Kind::UserDefined(user_defined) => user_defined.nullability,
-        #[expect(deprecated)]
-        r#type::Kind::UserDefinedTypeReference(_) => r#type::Nullability::Required as i32,
+        r#type::Kind::Unbound(_) => r#type::Nullability::Nullable as i32,
         r#type::Kind::Alias(alias) => alias.nullability,
     };
 
@@ -412,18 +381,6 @@ fn is_nullable(nullability: i32) -> datafusion::common::Result<bool> {
 #[cfg(test)]
 mod tests {
     use super::*;
-    use substrait::proto::r#type::Kind;
-
-    #[test]
-    fn type_is_nullable_user_defined_type_reference_is_required() {
-        // The deprecated `UserDefinedTypeReference` variant doesn't carry a
-        // nullability field; the consumer hardcodes Required (non-null).
-        #[expect(deprecated)]
-        let dt = Type {
-            kind: Some(Kind::UserDefinedTypeReference(0)),
-        };
-        assert!(!type_is_nullable(&dt).unwrap());
-    }
 
     #[test]
     fn type_is_nullable_missing_kind_defaults_to_nullable() {
diff --git a/datafusion/substrait/src/logical_plan/producer/expr/aggregate_function.rs b/datafusion/substrait/src/logical_plan/producer/expr/aggregate_function.rs
index 3713f8934f19f..ad8f57812f461 100644
--- a/datafusion/substrait/src/logical_plan/producer/expr/aggregate_function.rs
+++ b/datafusion/substrait/src/logical_plan/producer/expr/aggregate_function.rs
@@ -54,7 +54,6 @@ pub fn from_aggregate_function(
         });
     }
     let function_anchor = producer.register_function(func.name().to_string());
-    #[expect(deprecated)]
     Ok(Measure {
         measure: Some(AggregateFunction {
             function_reference: function_anchor,
@@ -66,7 +65,6 @@ pub fn from_aggregate_function(
                 false => AggregationInvocation::All as i32,
             },
             phase: AggregationPhase::Unspecified as i32,
-            args: vec![],
             options: vec![],
         }),
         filter: match filter {
diff --git a/datafusion/substrait/src/logical_plan/producer/expr/field_reference.rs b/datafusion/substrait/src/logical_plan/producer/expr/field_reference.rs
index 12ed92c64fe57..d12d825b9c206 100644
--- a/datafusion/substrait/src/logical_plan/producer/expr/field_reference.rs
+++ b/datafusion/substrait/src/logical_plan/producer/expr/field_reference.rs
@@ -19,6 +19,7 @@ use crate::logical_plan::producer::SubstraitProducer;
 use datafusion::common::{Column, DFSchemaRef, substrait_err};
 use datafusion::logical_expr::Expr;
 use substrait::proto::Expression;
+use substrait::proto::expression::field_reference::outer_reference::OuterReferenceType;
 use substrait::proto::expression::field_reference::{
     OuterReference, ReferenceType, RootReference, RootType,
 };
@@ -101,8 +102,11 @@ pub fn from_outer_reference_column(
         if let Some(index) = outer_schema.maybe_index_of_column(col) {
             return substrait_field_ref_with_root(
                 index,
+                #[expect(deprecated)]
                 RootType::OuterReference(OuterReference {
-                    steps_out: steps_out as u32,
+                    outer_reference_type: Some(OuterReferenceType::StepsOut(
+                        steps_out as u32,
+                    )),
                 }),
             );
         }
diff --git a/datafusion/substrait/src/logical_plan/producer/expr/literal.rs b/datafusion/substrait/src/logical_plan/producer/expr/literal.rs
index f26984ad4a394..2f808146778b1 100644
--- a/datafusion/substrait/src/logical_plan/producer/expr/literal.rs
+++ b/datafusion/substrait/src/logical_plan/producer/expr/literal.rs
@@ -26,7 +26,6 @@ use crate::variation_const::{
 use datafusion::arrow::array::{Array, GenericListArray, OffsetSizeTrait};
 use datafusion::arrow::temporal_conversions::NANOSECONDS;
 use datafusion::common::{ScalarValue, exec_err, not_impl_err};
-use substrait::proto::expression::literal::interval_day_to_second::PrecisionMode;
 use substrait::proto::expression::literal::map::KeyValue;
 use substrait::proto::expression::literal::{
     Decimal, IntervalCompound, IntervalDayToSecond, IntervalYearToMonth, List,
@@ -217,7 +216,7 @@ pub(crate) fn to_substrait_literal(
                     days: i.days,
                     seconds: (i.nanoseconds / NANOSECONDS) as i32,
                     subseconds: i.nanoseconds % NANOSECONDS,
-                    precision_mode: Some(PrecisionMode::Precision(9)), // nanoseconds
+                    precision: 9, // nanoseconds
                 }),
             }),
             DEFAULT_TYPE_VARIATION_REF,
@@ -227,7 +226,7 @@ pub(crate) fn to_substrait_literal(
                 days: i.days,
                 seconds: i.milliseconds / 1000,
                 subseconds: (i.milliseconds % 1000) as i64,
-                precision_mode: Some(PrecisionMode::Precision(3)), // 3 for milliseconds
+                precision: 3, // 3 for milliseconds
             }),
             DEFAULT_TYPE_VARIATION_REF,
         ),
diff --git a/datafusion/substrait/src/logical_plan/producer/expr/scalar_function.rs b/datafusion/substrait/src/logical_plan/producer/expr/scalar_function.rs
index 75720395aae7c..5736d1cc2b849 100644
--- a/datafusion/substrait/src/logical_plan/producer/expr/scalar_function.rs
+++ b/datafusion/substrait/src/logical_plan/producer/expr/scalar_function.rs
@@ -121,14 +121,12 @@ pub fn from_higher_order_function(
         output_field.is_nullable(),
     )?;
 
-    #[expect(deprecated)]
     Ok(Expression {
         rex_type: Some(RexType::ScalarFunction(ScalarFunction {
             function_reference: function_anchor,
             arguments,
             output_type: Some(output_type),
             options: vec![],
-            args: vec![],
         })),
     })
 }
@@ -152,14 +150,12 @@ fn from_function(
     let output_type = to_substrait_type(producer, output_type, output_nullability)?;
 
     let function_anchor = producer.register_function(name.to_string());
-    #[expect(deprecated)]
     Ok(Expression {
         rex_type: Some(RexType::ScalarFunction(ScalarFunction {
             function_reference: function_anchor,
             arguments,
             output_type: Some(output_type),
             options: vec![],
-            args: vec![],
         })),
     })
 }
@@ -288,13 +284,11 @@ fn make_substrait_like_expr(
         },
     ];
 
-    #[expect(deprecated)]
     let substrait_like = Expression {
         rex_type: Some(RexType::ScalarFunction(ScalarFunction {
             function_reference: function_anchor,
             arguments,
             output_type: None,
-            args: vec![],
             options: vec![],
         })),
     };
@@ -302,7 +296,6 @@ fn make_substrait_like_expr(
     if negated {
         let function_anchor = producer.register_function("not".to_string());
 
-        #[expect(deprecated)]
         Ok(Expression {
             rex_type: Some(RexType::ScalarFunction(ScalarFunction {
                 function_reference: function_anchor,
@@ -310,7 +303,6 @@ fn make_substrait_like_expr(
                     arg_type: Some(ArgType::Value(substrait_like)),
                 }],
                 output_type: None,
-                args: vec![],
                 options: vec![],
             })),
         })
@@ -338,7 +330,6 @@ fn to_substrait_unary_scalar_fn(
             }],
             output_type: Some(output_type.clone()),
             options: vec![],
-            ..Default::default()
         })),
     })
 }
@@ -352,7 +343,6 @@ pub fn make_binary_op_scalar_func(
     output_type: &Type,
 ) -> Expression {
     let function_anchor = producer.register_function(operator_to_name(op).to_string());
-    #[expect(deprecated)]
     Expression {
         rex_type: Some(RexType::ScalarFunction(ScalarFunction {
             function_reference: function_anchor,
@@ -365,7 +355,6 @@ pub fn make_binary_op_scalar_func(
                 },
             ],
             output_type: Some(output_type.clone()),
-            args: vec![],
             options: vec![],
         })),
     }
diff --git a/datafusion/substrait/src/logical_plan/producer/expr/window_function.rs b/datafusion/substrait/src/logical_plan/producer/expr/window_function.rs
index d35771bf099d3..4b3121e777501 100644
--- a/datafusion/substrait/src/logical_plan/producer/expr/window_function.rs
+++ b/datafusion/substrait/src/logical_plan/producer/expr/window_function.rs
@@ -17,15 +17,17 @@
 
 use crate::logical_plan::producer::SubstraitProducer;
 use crate::logical_plan::producer::utils::substrait_sort_field;
+use crate::variation_const::DEFAULT_TYPE_VARIATION_REF;
 use datafusion::common::{DFSchemaRef, ScalarValue, not_impl_err};
 use datafusion::logical_expr::expr::{WindowFunction, WindowFunctionParams};
 use datafusion::logical_expr::{WindowFrame, WindowFrameBound, WindowFrameUnits};
 use substrait::proto::aggregate_function::AggregationInvocation;
-use substrait::proto::expression::RexType;
 use substrait::proto::expression::WindowFunction as SubstraitWindowFunction;
+use substrait::proto::expression::literal::LiteralType;
 use substrait::proto::expression::window_function::bound as SubstraitBound;
 use substrait::proto::expression::window_function::bound::Kind as BoundKind;
 use substrait::proto::expression::window_function::{Bound, BoundsType};
+use substrait::proto::expression::{Literal, RexType};
 use substrait::proto::function_argument::ArgType;
 use substrait::proto::{Expression, FunctionArgument, SortField};
 
@@ -99,9 +101,8 @@ fn make_substrait_window_function(
     bounds_type: BoundsType,
     distinct: bool,
 ) -> Expression {
-    #[expect(deprecated)]
     Expression {
-        rex_type: Some(RexType::WindowFunction(SubstraitWindowFunction {
+        rex_type: Some(RexType::WindowFunction(Box::new(SubstraitWindowFunction {
             function_reference,
             arguments,
             partitions,
@@ -114,11 +115,10 @@ fn make_substrait_window_function(
             } else {
                 AggregationInvocation::All as i32
             },
-            lower_bound: Some(bounds.0),
-            upper_bound: Some(bounds.1),
-            args: vec![],
+            lower_bound: Some(Box::new(bounds.0)),
+            upper_bound: Some(Box::new(bounds.1)),
             bounds_type: bounds_type as i32,
-        })),
+        }))),
     }
 }
 
@@ -152,16 +152,56 @@ fn to_substrait_bound(bound: &WindowFrameBound) -> datafusion::common::Result<Bo
         WindowFrameBound::CurrentRow => Ok(Bound {
             kind: Some(BoundKind::CurrentRow(SubstraitBound::CurrentRow {})),
         }),
-        WindowFrameBound::Preceding(s) => Ok(Bound {
-            kind: Some(BoundKind::Preceding(SubstraitBound::Preceding {
-                offset: to_substrait_bound_offset(s)?,
-            })),
-        }),
-        WindowFrameBound::Following(s) => Ok(Bound {
-            kind: Some(BoundKind::Following(SubstraitBound::Following {
-                offset: to_substrait_bound_offset(s)?,
-            })),
-        }),
+        WindowFrameBound::Preceding(s) => {
+            let offset = to_substrait_bound_offset(s)?;
+            if offset == 0 {
+                // A zero distance is equivalent to CurrentRow, and `offset`
+                // cannot represent zero, so the specification asks producers to
+                // emit CurrentRow instead of a zero bound.
+                return Ok(Bound {
+                    kind: Some(BoundKind::CurrentRow(SubstraitBound::CurrentRow {})),
+                });
+            }
+            #[expect(deprecated)]
+            Ok(Bound {
+                kind: Some(BoundKind::Preceding(Box::new(SubstraitBound::Preceding {
+                    // `offset` carries the int64-literal equivalent for
+                    // consumers that do not read `offset_expr` yet.
+                    offset,
+                    offset_expr: Some(Box::new(bound_offset_expr(offset))),
+                }))),
+            })
+        }
+        WindowFrameBound::Following(s) => {
+            let offset = to_substrait_bound_offset(s)?;
+            if offset == 0 {
+                // A zero distance is equivalent to CurrentRow, and `offset`
+                // cannot represent zero, so the specification asks producers to
+                // emit CurrentRow instead of a zero bound.
+                return Ok(Bound {
+                    kind: Some(BoundKind::CurrentRow(SubstraitBound::CurrentRow {})),
+                });
+            }
+            #[expect(deprecated)]
+            Ok(Bound {
+                kind: Some(BoundKind::Following(Box::new(SubstraitBound::Following {
+                    offset,
+                    offset_expr: Some(Box::new(bound_offset_expr(offset))),
+                }))),
+            })
+        }
+    }
+}
+
+/// Builds the int64 literal expression that a window frame bound offset carries
+/// in `offset_expr`.
+fn bound_offset_expr(offset: i64) -> Expression {
+    Expression {
+        rex_type: Some(RexType::Literal(Literal {
+            nullable: false,
+            type_variation_reference: DEFAULT_TYPE_VARIATION_REF,
+            literal_type: Some(LiteralType::I64(offset)),
+        })),
     }
 }
 
@@ -188,6 +228,25 @@ mod tests {
     use datafusion::common::assert_contains;
 
     #[test]
+    fn zero_distance_bounds_become_current_row() {
+        // `offset` cannot represent zero and the specification asks producers to
+        // emit CurrentRow rather than a zero bound, so neither field is written.
+        let frame = WindowFrame::new_bounds(
+            WindowFrameUnits::Rows,
+            WindowFrameBound::Preceding(ScalarValue::UInt64(Some(0))),
+            WindowFrameBound::Following(ScalarValue::UInt64(Some(0))),
+        );
+        let (lower, upper) = to_substrait_bounds(&frame).unwrap();
+        for bound in [lower, upper] {
+            assert_eq!(
+                bound.kind,
+                Some(BoundKind::CurrentRow(SubstraitBound::CurrentRow {}))
+            );
+        }
+    }
+
+    #[test]
+    #[expect(deprecated)]
     fn window_frame_offsets() {
         for value in [
             ScalarValue::UInt8(Some(1)),
@@ -207,9 +266,10 @@ mod tests {
             let (_, bound) = to_substrait_bounds(&frame).unwrap();
             assert_eq!(
                 bound.kind,
-                Some(BoundKind::Following(SubstraitBound::Following {
-                    offset: 1
-                }))
+                Some(BoundKind::Following(Box::new(SubstraitBound::Following {
+                    offset: 1,
+                    offset_expr: Some(Box::new(bound_offset_expr(1))),
+                })))
             );
         }
 
diff --git a/datafusion/substrait/src/logical_plan/producer/plan.rs b/datafusion/substrait/src/logical_plan/producer/plan.rs
index 3b58720dba832..f6bdaa3e69fa7 100644
--- a/datafusion/substrait/src/logical_plan/producer/plan.rs
+++ b/datafusion/substrait/src/logical_plan/producer/plan.rs
@@ -20,7 +20,7 @@ use crate::logical_plan::producer::{
 };
 use datafusion::execution::SessionState;
 use datafusion::logical_expr::{LogicalPlan, SubqueryAlias};
-use substrait::proto::{Plan, PlanRel, Rel, RelRoot, plan_rel};
+use substrait::proto::{ExecutionBehavior, Plan, PlanRel, Rel, RelRoot, plan_rel};
 use substrait::version;
 
 /// Convert DataFusion LogicalPlan to Substrait Plan
@@ -51,6 +51,9 @@ pub fn to_substrait_plan(
         expected_type_urls: vec![],
         parameter_bindings: vec![],
         type_aliases: vec![],
+        // DataFusion does not emit execution context variables, so the
+        // evaluation mode does not govern anything in the plans it produces.
+        execution_behavior: Some(ExecutionBehavior::default()),
     }))
 }
 
diff --git a/datafusion/substrait/src/logical_plan/producer/rel/aggregate_rel.rs b/datafusion/substrait/src/logical_plan/producer/rel/aggregate_rel.rs
index dec94b0422257..d31a0a9809eda 100644
--- a/datafusion/substrait/src/logical_plan/producer/rel/aggregate_rel.rs
+++ b/datafusion/substrait/src/logical_plan/producer/rel/aggregate_rel.rs
@@ -64,15 +64,16 @@ pub fn from_distinct(
                 .map(substrait_field_ref)
                 .collect::<datafusion::common::Result<Vec<_>>>()?;
 
-            #[expect(deprecated)]
+            // The keys are declared once on the relation and the single grouping
+            // set references them by index.
+            let expression_references = (0..grouping.len() as u32).collect();
             Ok(Box::new(Rel {
                 rel_type: Some(RelType::Aggregate(Box::new(AggregateRel {
                     common: None,
                     input: Some(input),
-                    grouping_expressions: vec![],
+                    grouping_expressions: grouping,
                     groupings: vec![Grouping {
-                        grouping_expressions: grouping,
-                        expression_references: vec![],
+                        expression_references,
                     }],
                     measures: vec![],
                     advanced_extension: None,
@@ -160,17 +161,13 @@ pub fn parse_flat_grouping_exprs(
     ref_group_exprs: &mut Vec<Expression>,
 ) -> datafusion::common::Result<Grouping> {
     let mut expression_references = vec![];
-    let mut grouping_expressions = vec![];
 
     for e in exprs {
         let rex = producer.handle_expr(e, schema)?;
-        grouping_expressions.push(rex.clone());
         ref_group_exprs.push(rex);
         expression_references.push((ref_group_exprs.len() - 1) as u32);
     }
-    #[expect(deprecated)]
     Ok(Grouping {
-        grouping_expressions,
         expression_references,
     })
 }
diff --git a/datafusion/substrait/src/logical_plan/producer/rel/fetch_rel.rs b/datafusion/substrait/src/logical_plan/producer/rel/fetch_rel.rs
index e878b3816ff42..76418af562c6a 100644
--- a/datafusion/substrait/src/logical_plan/producer/rel/fetch_rel.rs
+++ b/datafusion/substrait/src/logical_plan/producer/rel/fetch_rel.rs
@@ -20,7 +20,7 @@ use datafusion::common::DFSchema;
 use datafusion::logical_expr::Limit;
 use std::sync::Arc;
 use substrait::proto::rel::RelType;
-use substrait::proto::{FetchRel, Rel, fetch_rel};
+use substrait::proto::{FetchRel, Rel};
 
 pub fn from_limit(
     producer: &mut impl SubstraitProducer,
@@ -28,26 +28,24 @@ pub fn from_limit(
 ) -> datafusion::common::Result<Box<Rel>> {
     let input = producer.handle_plan(limit.input.as_ref())?;
     let empty_schema = Arc::new(DFSchema::empty());
-    let offset_mode = limit
+    let offset_expr = limit
         .skip
         .as_ref()
         .map(|expr| producer.handle_expr(expr.as_ref(), &empty_schema))
         .transpose()?
-        .map(Box::new)
-        .map(fetch_rel::OffsetMode::OffsetExpr);
-    let count_mode = limit
+        .map(Box::new);
+    let count_expr = limit
         .fetch
         .as_ref()
         .map(|expr| producer.handle_expr(expr.as_ref(), &empty_schema))
         .transpose()?
-        .map(Box::new)
-        .map(fetch_rel::CountMode::CountExpr);
+        .map(Box::new);
     Ok(Box::new(Rel {
         rel_type: Some(RelType::Fetch(Box::new(FetchRel {
             common: None,
             input: Some(input),
-            offset_mode,
-            count_mode,
+            offset_expr,
+            count_expr,
             advanced_extension: None,
         }))),
     }))
diff --git a/datafusion/substrait/src/logical_plan/producer/rel/project_rel.rs b/datafusion/substrait/src/logical_plan/producer/rel/project_rel.rs
index 33920cdf86f7a..d610704e5bb82 100644
--- a/datafusion/substrait/src/logical_plan/producer/rel/project_rel.rs
+++ b/datafusion/substrait/src/logical_plan/producer/rel/project_rel.rs
@@ -39,6 +39,7 @@ pub fn from_projection(
     let common = RelCommon {
         emit_kind: Some(emit_kind),
         hint: None,
+        rel_anchor: None,
         advanced_extension: None,
     };
 
@@ -73,6 +74,7 @@ pub fn from_window(
     let common = RelCommon {
         emit_kind: Some(emit_kind),
         hint: None,
+        rel_anchor: None,
         advanced_extension: None,
     };
     let project_rel = Box::new(ProjectRel {
diff --git a/datafusion/substrait/src/logical_plan/producer/rel/read_rel.rs b/datafusion/substrait/src/logical_plan/producer/rel/read_rel.rs
index 900273bf8e6d7..a12460f785a46 100644
--- a/datafusion/substrait/src/logical_plan/producer/rel/read_rel.rs
+++ b/datafusion/substrait/src/logical_plan/producer/rel/read_rel.rs
@@ -144,7 +144,6 @@ pub fn from_empty_relation(
 
         ReadType::VirtualTable(VirtualTable {
             expressions: vec![NestedStruct { fields }],
-            ..Default::default()
         })
     } else {
         ReadType::VirtualTable(VirtualTable::default())
@@ -178,10 +177,7 @@ pub fn from_values(
             best_effort_filter: None,
             projection: None,
             advanced_extension: None,
-            read_type: Some(ReadType::VirtualTable(VirtualTable {
-                expressions,
-                ..Default::default()
-            })),
+            read_type: Some(ReadType::VirtualTable(VirtualTable { expressions })),
         }))),
     }))
 }
diff --git a/datafusion/substrait/src/logical_plan/producer/rel/sort_rel.rs b/datafusion/substrait/src/logical_plan/producer/rel/sort_rel.rs
index d4520a4c37b14..43d27ea792e69 100644
--- a/datafusion/substrait/src/logical_plan/producer/rel/sort_rel.rs
+++ b/datafusion/substrait/src/logical_plan/producer/rel/sort_rel.rs
@@ -21,7 +21,7 @@ use datafusion::logical_expr::Sort;
 use substrait::proto::expression::literal::LiteralType;
 use substrait::proto::expression::{Literal, RexType};
 use substrait::proto::rel::RelType;
-use substrait::proto::{Expression, FetchRel, Rel, SortRel, fetch_rel};
+use substrait::proto::{Expression, FetchRel, Rel, SortRel};
 
 pub fn from_sort(
     producer: &mut impl SubstraitProducer,
@@ -46,20 +46,19 @@ pub fn from_sort(
 
     match fetch {
         Some(amount) => {
-            let count_mode =
-                Some(fetch_rel::CountMode::CountExpr(Box::new(Expression {
-                    rex_type: Some(RexType::Literal(Literal {
-                        nullable: false,
-                        type_variation_reference: DEFAULT_TYPE_VARIATION_REF,
-                        literal_type: Some(LiteralType::I64(*amount as i64)),
-                    })),
-                })));
+            let count_expr = Some(Box::new(Expression {
+                rex_type: Some(RexType::Literal(Literal {
+                    nullable: false,
+                    type_variation_reference: DEFAULT_TYPE_VARIATION_REF,
+                    literal_type: Some(LiteralType::I64(*amount as i64)),
+                })),
+            }));
             Ok(Box::new(Rel {
                 rel_type: Some(RelType::Fetch(Box::new(FetchRel {
                     common: None,
                     input: Some(sort_rel),
-                    offset_mode: None,
-                    count_mode,
+                    offset_expr: None,
+                    count_expr,
                     advanced_extension: None,
                 }))),
             }))
diff --git a/datafusion/substrait/src/logical_plan/producer/utils.rs b/datafusion/substrait/src/logical_plan/producer/utils.rs
index e8310f4acd31e..13984eb6b5d5a 100644
--- a/datafusion/substrait/src/logical_plan/producer/utils.rs
+++ b/datafusion/substrait/src/logical_plan/producer/utils.rs
@@ -93,7 +93,6 @@ pub(crate) fn negate(
 ) -> Expression {
     let function_anchor = producer.register_function("not".to_string());
 
-    #[expect(deprecated)]
     Expression {
         rex_type: Some(substrait::proto::expression::RexType::ScalarFunction(
             substrait::proto::expression::ScalarFunction {
@@ -104,7 +103,6 @@ pub(crate) fn negate(
                     )),
                 }],
                 output_type: None,
-                args: vec![],
                 options: vec![],
             },
         )),
diff --git a/datafusion/substrait/tests/testdata/test_plans/aggregate_identical_grouping_expressions.substrait.json b/datafusion/substrait/tests/testdata/test_plans/aggregate_identical_grouping_expressions.substrait.json
index 15c0b0505fa68..2901f7e537ed7 100644
--- a/datafusion/substrait/tests/testdata/test_plans/aggregate_identical_grouping_expressions.substrait.json
+++ b/datafusion/substrait/tests/testdata/test_plans/aggregate_identical_grouping_expressions.substrait.json
@@ -25,18 +25,19 @@
             },
             "groupings": [
               {
-                "groupingExpressions": [
-                  {
-                    "literal": {
-                      "i32": 1
-                    }
-                  },
-                  {
-                    "literal": {
-                      "i32": 1
-                    }
-                  }
-                ]
+                "expressionReferences": [0, 1]
+              }
+            ],
+            "groupingExpressions": [
+              {
+                "literal": {
+                  "i32": 1
+                }
+              },
+              {
+                "literal": {
+                  "i32": 1
+                }
               }
             ],
             "measures": []
diff --git a/datafusion/substrait/tests/testdata/test_plans/aggregate_identical_measures.substrait.json b/datafusion/substrait/tests/testdata/test_plans/aggregate_identical_measures.substrait.json
index 620d55e93ee1e..5186ace7f1e03 100644
--- a/datafusion/substrait/tests/testdata/test_plans/aggregate_identical_measures.substrait.json
+++ b/datafusion/substrait/tests/testdata/test_plans/aggregate_identical_measures.substrait.json
@@ -39,8 +39,9 @@
             }
           },
           "groupings": [{
-            "groupingExpressions": []
+            "expressionReferences": []
           }],
+          "groupingExpressions": [],
           "measures": [
             {
               "measure": {
diff --git a/datafusion/substrait/tests/testdata/test_plans/aggregate_no_project.substrait.json b/datafusion/substrait/tests/testdata/test_plans/aggregate_no_project.substrait.json
index ed8675b968269..1394e3ca2bbf9 100644
--- a/datafusion/substrait/tests/testdata/test_plans/aggregate_no_project.substrait.json
+++ b/datafusion/substrait/tests/testdata/test_plans/aggregate_no_project.substrait.json
@@ -46,15 +46,8 @@
             },
             "groupings": [
               {
-                "groupingExpressions": [
-                  {
-                    "selection": {
-                      "directReference": {
-                        "structField": {}
-                      },
-                      "rootReference": {}
-                    }
-                  }
+                "expressionReferences": [
+                  0
                 ]
               }
             ],
@@ -80,6 +73,16 @@
                   ]
                 }
               }
+            ],
+            "groupingExpressions": [
+              {
+                "selection": {
+                  "directReference": {
+                    "structField": {}
+                  },
+                  "rootReference": {}
+                }
+              }
             ]
           }
         },
diff --git a/datafusion/substrait/tests/testdata/test_plans/aggregate_sorted_no_project.substrait.json b/datafusion/substrait/tests/testdata/test_plans/aggregate_sorted_no_project.substrait.json
index d5170223cd65b..2ef9c86eee2c0 100644
--- a/datafusion/substrait/tests/testdata/test_plans/aggregate_sorted_no_project.substrait.json
+++ b/datafusion/substrait/tests/testdata/test_plans/aggregate_sorted_no_project.substrait.json
@@ -46,16 +46,17 @@
             },
             "groupings": [
               {
-                "groupingExpressions": [
-                  {
-                    "selection": {
-                      "directReference": {
-                        "structField": {}
-                      },
-                      "rootReference": {}
-                    }
-                  }
-                ]
+                "expressionReferences": [0]
+              }
+            ],
+            "groupingExpressions": [
+              {
+                "selection": {
+                  "directReference": {
+                    "structField": {}
+                  },
+                  "rootReference": {}
+                }
               }
             ],
             "measures": [
diff --git a/datafusion/substrait/tests/testdata/test_plans/join_with_expression_key.json b/datafusion/substrait/tests/testdata/test_plans/join_with_expression_key.json
index 8a81a9a0c780f..f1cda34c7715a 100644
--- a/datafusion/substrait/tests/testdata/test_plans/join_with_expression_key.json
+++ b/datafusion/substrait/tests/testdata/test_plans/join_with_expression_key.json
@@ -226,28 +226,29 @@
                     }
                   },
                   "groupings": [{
-                    "groupingExpressions": [{
-                      "selection": {
-                        "directReference": {
-                          "structField": {
-                            "field": 1
-                          }
-                        },
-                        "rootReference": {
-                        }
+                    "expressionReferences": [0, 1]
+                  }],
+                  "groupingExpressions": [{
+                  "selection": {
+                    "directReference": {
+                      "structField": {
+                        "field": 1
                       }
-                    }, {
-                      "selection": {
-                        "directReference": {
-                          "structField": {
-                            "field": 2
-                          }
-                        },
-                        "rootReference": {
-                        }
+                    },
+                    "rootReference": {
+                    }
+                  }
+                }, {
+                  "selection": {
+                    "directReference": {
+                      "structField": {
+                        "field": 2
                       }
-                    }]
-                  }],
+                    },
+                    "rootReference": {
+                    }
+                  }
+                }],
                   "measures": [{
                     "measure": {
                       "functionReference": 2,
@@ -531,28 +532,29 @@
                                     }
                                   },
                                   "groupings": [{
-                                    "groupingExpressions": [{
-                                      "selection": {
-                                        "directReference": {
-                                          "structField": {
-                                            "field": 1
-                                          }
-                                        },
-                                        "rootReference": {
-                                        }
+                                    "expressionReferences": [0, 1]
+                                  }],
+                                  "groupingExpressions": [{
+                                  "selection": {
+                                    "directReference": {
+                                      "structField": {
+                                        "field": 1
                                       }
-                                    }, {
-                                      "selection": {
-                                        "directReference": {
-                                          "structField": {
-                                            "field": 2
-                                          }
-                                        },
-                                        "rootReference": {
-                                        }
+                                    },
+                                    "rootReference": {
+                                    }
+                                  }
+                                }, {
+                                  "selection": {
+                                    "directReference": {
+                                      "structField": {
+                                        "field": 2
                                       }
-                                    }]
-                                  }],
+                                    },
+                                    "rootReference": {
+                                    }
+                                  }
+                                }],
                                   "measures": [{
                                     "measure": {
                                       "functionReference": 2,
@@ -679,18 +681,19 @@
                     }
                   },
                   "groupings": [{
-                    "groupingExpressions": [{
-                      "selection": {
-                        "directReference": {
-                          "structField": {
-                            "field": 1
-                          }
-                        },
-                        "rootReference": {
-                        }
-                      }
-                    }]
+                    "expressionReferences": [0]
                   }],
+                  "groupingExpressions": [{
+                  "selection": {
+                    "directReference": {
+                      "structField": {
+                        "field": 1
+                      }
+                    },
+                    "rootReference": {
+                    }
+                  }
+                }],
                   "measures": [{
                     "measure": {
                       "functionReference": 2,
diff --git a/datafusion/substrait/tests/testdata/test_plans/multilayer_aggregate.substrait.json b/datafusion/substrait/tests/testdata/test_plans/multilayer_aggregate.substrait.json
index 1f47b916daf0f..3e5f9f4aedc6f 100644
--- a/datafusion/substrait/tests/testdata/test_plans/multilayer_aggregate.substrait.json
+++ b/datafusion/substrait/tests/testdata/test_plans/multilayer_aggregate.substrait.json
@@ -52,43 +52,27 @@
                   "input": {
                     "read": {
                       "common": {
-                        "direct": {}
+                        "direct": {
+                        }
                       },
                       "baseSchema": {
-                        "names": [
-                          "product"
-                        ],
+                        "names": ["product"],
                         "struct": {
-                          "types": [
-                            {
-                              "string": {
-                                "nullability": "NULLABILITY_REQUIRED"
-                              }
+                          "types": [{
+                            "string": {
+                              "nullability": "NULLABILITY_REQUIRED"
                             }
-                          ],
+                          }],
                           "nullability": "NULLABILITY_REQUIRED"
                         }
                       },
                       "namedTable": {
-                        "names": [
-                          "sales"
-                        ]
+                        "names": ["sales"]
                       }
                     }
                   },
                   "groupings": [{
-                    "groupingExpressions": [{
-                      "selection": {
-                        "directReference": {
-                          "structField": {
-                            "field": 0
-                          }
-                        },
-                        "rootReference": {
-                        }
-                      }
-                    }],
-                    "expressionReferences": []
+                    "expressionReferences": [0]
                   }],
                   "measures": [{
                     "measure": {
@@ -119,22 +103,21 @@
                       "options": []
                     }
                   }],
-                  "groupingExpressions": []
+                  "groupingExpressions": [{
+                    "selection": {
+                      "directReference": {
+                        "structField": {
+                          "field": 0
+                        }
+                      },
+                      "rootReference": {
+                      }
+                    }
+                  }]
                 }
               },
               "groupings": [{
-                "groupingExpressions": [{
-                  "selection": {
-                    "directReference": {
-                      "structField": {
-                        "field": 0
-                      }
-                    },
-                    "rootReference": {
-                    }
-                  }
-                }],
-                "expressionReferences": []
+                "expressionReferences": [0]
               }],
               "measures": [{
                 "measure": {
@@ -165,7 +148,17 @@
                   "options": []
                 }
               }],
-              "groupingExpressions": []
+              "groupingExpressions": [{
+                "selection": {
+                  "directReference": {
+                    "structField": {
+                      "field": 0
+                    }
+                  },
+                  "rootReference": {
+                  }
+                }
+              }]
             }
           },
           "expressions": [{
diff --git a/datafusion/substrait/tests/testdata/test_plans/multiple_joins.json b/datafusion/substrait/tests/testdata/test_plans/multiple_joins.json
index 15c0313b43b54..7de3d1d042562 100644
--- a/datafusion/substrait/tests/testdata/test_plans/multiple_joins.json
+++ b/datafusion/substrait/tests/testdata/test_plans/multiple_joins.json
@@ -72,46 +72,28 @@
                                 }
                               },
                               "virtualTable": {
-                                "expressions": [
-                                  {
-                                    "fields": [
-                                      {
-                                        "literal": {
-                                          "i64": "1",
-                                          "nullable": true,
-                                          "typeVariationReference": 0
-                                        }
-                                      }
-                                    ]
-                                  },
-                                  {
-                                    "fields": [
-                                      {
-                                        "literal": {
-                                          "i64": "2",
-                                          "nullable": true,
-                                          "typeVariationReference": 0
-                                        }
-                                      }
-                                    ]
-                                  }
-                                ]
+                                "expressions": [{
+                                  "fields": [{
+                                    "literal": {
+                                      "i64": "1",
+                                      "nullable": true,
+                                      "typeVariationReference": 0
+                                    }
+                                  }]
+                                }, {
+                                  "fields": [{
+                                    "literal": {
+                                      "i64": "2",
+                                      "nullable": true,
+                                      "typeVariationReference": 0
+                                    }
+                                  }]
+                                }]
                               }
                             }
                           },
                           "groupings": [{
-                            "groupingExpressions": [{
-                              "selection": {
-                                "directReference": {
-                                  "structField": {
-                                    "field": 0
-                                  }
-                                },
-                                "rootReference": {
-                                }
-                              }
-                            }],
-                            "expressionReferences": []
+                            "expressionReferences": [0]
                           }],
                           "measures": [{
                             "measure": {
@@ -130,7 +112,17 @@
                               "options": []
                             }
                           }],
-                          "groupingExpressions": []
+                          "groupingExpressions": [{
+                            "selection": {
+                              "directReference": {
+                                "structField": {
+                                  "field": 0
+                                }
+                              },
+                              "rootReference": {
+                              }
+                            }
+                          }]
                         }
                       },
                       "right": {
@@ -164,73 +156,63 @@
                                 }
                               },
                               "virtualTable": {
-                                "expressions": [
-                                  {
-                                    "fields": [
-                                      {
-                                        "literal": {
-                                          "i64": "1",
-                                          "nullable": true,
-                                          "typeVariationReference": 0
-                                        }
-                                      },
-                                      {
-                                        "literal": {
-                                          "string": "info",
-                                          "nullable": true,
-                                          "typeVariationReference": 0
-                                        }
-                                      }
-                                    ]
-                                  },
-                                  {
-                                    "fields": [
-                                      {
-                                        "literal": {
-                                          "i64": "2",
-                                          "nullable": true,
-                                          "typeVariationReference": 0
-                                        }
-                                      },
-                                      {
-                                        "literal": {
-                                          "string": "low",
-                                          "nullable": true,
-                                          "typeVariationReference": 0
-                                        }
-                                      }
-                                    ]
-                                  }
-                                ]
+                                "expressions": [{
+                                  "fields": [{
+                                    "literal": {
+                                      "i64": "1",
+                                      "nullable": true,
+                                      "typeVariationReference": 0
+                                    }
+                                  }, {
+                                    "literal": {
+                                      "string": "info",
+                                      "nullable": true,
+                                      "typeVariationReference": 0
+                                    }
+                                  }]
+                                }, {
+                                  "fields": [{
+                                    "literal": {
+                                      "i64": "2",
+                                      "nullable": true,
+                                      "typeVariationReference": 0
+                                    }
+                                  }, {
+                                    "literal": {
+                                      "string": "low",
+                                      "nullable": true,
+                                      "typeVariationReference": 0
+                                    }
+                                  }]
+                                }]
                               }
                             }
                           },
                           "groupings": [{
-                            "groupingExpressions": [{
-                              "selection": {
-                                "directReference": {
-                                  "structField": {
-                                    "field": 0
-                                  }
-                                },
-                                "rootReference": {
+                            "expressionReferences": [0, 1]
+                          }],
+                          "measures": [],
+                          "groupingExpressions": [{
+                            "selection": {
+                              "directReference": {
+                                "structField": {
+                                  "field": 0
                                 }
+                              },
+                              "rootReference": {
                               }
-                            }, {
-                              "selection": {
-                                "directReference": {
-                                  "structField": {
-                                    "field": 1
-                                  }
-                                },
-                                "rootReference": {
+                            }
+                          }, {
+                            "selection": {
+                              "directReference": {
+                                "structField": {
+                                  "field": 1
                                 }
+                              },
+                              "rootReference": {
                               }
-                            }],
-                            "expressionReferences": []
-                          }],
-                          "measures": [],
-                          "groupingExpressions": []
+                            }
+                          }]
                         }
                       },
                       "expression": {
@@ -300,46 +282,28 @@
                             }
                           },
                           "virtualTable": {
-                            "expressions": [
-                              {
-                                "fields": [
-                                  {
-                                    "literal": {
-                                      "i64": "1",
-                                      "nullable": true,
-                                      "typeVariationReference": 0
-                                    }
-                                  }
-                                ]
-                              },
-                              {
-                                "fields": [
-                                  {
-                                    "literal": {
-                                      "i64": "2",
-                                      "nullable": true,
-                                      "typeVariationReference": 0
-                                    }
-                                  }
-                                ]
-                              }
-                            ]
+                            "expressions": [{
+                              "fields": [{
+                                "literal": {
+                                  "i64": "1",
+                                  "nullable": true,
+                                  "typeVariationReference": 0
+                                }
+                              }]
+                            }, {
+                              "fields": [{
+                                "literal": {
+                                  "i64": "2",
+                                  "nullable": true,
+                                  "typeVariationReference": 0
+                                }
+                              }]
+                            }]
                           }
                         }
                       },
                       "groupings": [{
-                        "groupingExpressions": [{
-                          "selection": {
-                            "directReference": {
-                              "structField": {
-                                "field": 0
-                              }
-                            },
-                            "rootReference": {
-                            }
-                          }
-                        }],
-                        "expressionReferences": []
+                        "expressionReferences": [0]
                       }],
                       "measures": [{
                         "measure": {
@@ -358,7 +322,17 @@
                           "options": []
                         }
                       }],
-                      "groupingExpressions": []
+                      "groupingExpressions": [{
+                        "selection": {
+                          "directReference": {
+                            "structField": {
+                              "field": 0
+                            }
+                          },
+                          "rootReference": {
+                          }
+                        }
+                      }]
                     }
                   },
                   "expression": {
@@ -428,46 +402,28 @@
                         }
                       },
                       "virtualTable": {
-                        "expressions": [
-                          {
-                            "fields": [
-                              {
-                                "literal": {
-                                  "i64": "1",
-                                  "nullable": true,
-                                  "typeVariationReference": 0
-                                }
-                              }
-                            ]
-                          },
-                          {
-                            "fields": [
-                              {
-                                "literal": {
-                                  "i64": "2",
-                                  "nullable": true,
-                                  "typeVariationReference": 0
-                                }
-                              }
-                            ]
-                          }
-                        ]
+                        "expressions": [{
+                          "fields": [{
+                            "literal": {
+                              "i64": "1",
+                              "nullable": true,
+                              "typeVariationReference": 0
+                            }
+                          }]
+                        }, {
+                          "fields": [{
+                            "literal": {
+                              "i64": "2",
+                              "nullable": true,
+                              "typeVariationReference": 0
+                            }
+                          }]
+                        }]
                       }
                     }
                   },
                   "groupings": [{
-                    "groupingExpressions": [{
-                      "selection": {
-                        "directReference": {
-                          "structField": {
-                            "field": 0
-                          }
-                        },
-                        "rootReference": {
-                        }
-                      }
-                    }],
-                    "expressionReferences": []
+                    "expressionReferences": [0]
                   }],
                   "measures": [{
                     "measure": {
@@ -486,7 +442,17 @@
                       "options": []
                     }
                   }],
-                  "groupingExpressions": []
+                  "groupingExpressions": [{
+                    "selection": {
+                      "directReference": {
+                        "structField": {
+                          "field": 0
+                        }
+                      },
+                      "rootReference": {
+                      }
+                    }
+                  }]
                 }
               },
               "expression": {
diff --git a/datafusion/substrait/tests/testdata/test_plans/select_count_from_select_1.substrait.json b/datafusion/substrait/tests/testdata/test_plans/select_count_from_select_1.substrait.json
index b0d4ba4813bcf..9e223e16e38f1 100644
--- a/datafusion/substrait/tests/testdata/test_plans/select_count_from_select_1.substrait.json
+++ b/datafusion/substrait/tests/testdata/test_plans/select_count_from_select_1.substrait.json
@@ -60,7 +60,6 @@
             },
             "groupings": [
               {
-                "groupingExpressions": [],
                 "expressionReferences": []
               }
             ],
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_01_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_01_plan.json
index 3738a50a62382..b51e4996f657e 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_01_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_01_plan.json
@@ -472,26 +472,7 @@
                 }
               },
               "groupings": [{
-                "groupingExpressions": [{
-                  "selection": {
-                    "directReference": {
-                      "structField": {
-                      }
-                    },
-                    "rootReference": {
-                    }
-                  }
-                }, {
-                  "selection": {
-                    "directReference": {
-                      "structField": {
-                        "field": 1
-                      }
-                    },
-                    "rootReference": {
-                    }
-                  }
-                }]
+                "expressionReferences": [0, 1]
               }],
               "measures": [{
                 "measure": {
@@ -686,6 +667,26 @@
                   },
                   "invocation": "AGGREGATION_INVOCATION_ALL"
                 }
+              }],
+              "groupingExpressions": [{
+                "selection": {
+                  "directReference": {
+                    "structField": {
+                    }
+                  },
+                  "rootReference": {
+                  }
+                }
+              }, {
+                "selection": {
+                  "directReference": {
+                    "structField": {
+                      "field": 1
+                    }
+                  },
+                  "rootReference": {
+                  }
+                }
               }]
             }
           },
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_02_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_02_plan.json
index f6c5e802a5e36..20ce5529da83f 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_02_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_02_plan.json
@@ -1148,7 +1148,11 @@
               }]
             }
           },
-          "count": "100"
+          "countExpr": {
+            "literal": {
+              "i64": "100"
+            }
+          }
         }
       },
       "names": ["S_ACCTBAL", "S_NAME", "N_NAME", "P_PARTKEY", "P_MFGR", "S_ADDRESS", "S_PHONE", "S_COMMENT"]
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_03_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_03_plan.json
index d4dea1d03c466..e90059e784353 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_03_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_03_plan.json
@@ -602,36 +602,7 @@
                         }
                       },
                       "groupings": [{
-                        "groupingExpressions": [{
-                          "selection": {
-                            "directReference": {
-                              "structField": {
-                              }
-                            },
-                            "rootReference": {
-                            }
-                          }
-                        }, {
-                          "selection": {
-                            "directReference": {
-                              "structField": {
-                                "field": 1
-                              }
-                            },
-                            "rootReference": {
-                            }
-                          }
-                        }, {
-                          "selection": {
-                            "directReference": {
-                              "structField": {
-                                "field": 2
-                              }
-                            },
-                            "rootReference": {
-                            }
-                          }
-                        }]
+                        "expressionReferences": [0, 1, 2]
                       }],
                       "measures": [{
                         "measure": {
@@ -659,6 +630,36 @@
                             }
                           }]
                         }
+                      }],
+                      "groupingExpressions": [{
+                        "selection": {
+                          "directReference": {
+                            "structField": {
+                            }
+                          },
+                          "rootReference": {
+                          }
+                        }
+                      }, {
+                        "selection": {
+                          "directReference": {
+                            "structField": {
+                              "field": 1
+                            }
+                          },
+                          "rootReference": {
+                          }
+                        }
+                      }, {
+                        "selection": {
+                          "directReference": {
+                            "structField": {
+                              "field": 2
+                            }
+                          },
+                          "rootReference": {
+                          }
+                        }
                       }]
                     }
                   },
@@ -733,7 +734,11 @@
               }]
             }
           },
-          "count": "10"
+          "countExpr": {
+            "literal": {
+              "i64": "10"
+            }
+          }
         }
       },
       "names": ["L_ORDERKEY", "REVENUE", "O_ORDERDATE", "O_SHIPPRIORITY"]
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_04_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_04_plan.json
index 3e665f50f3207..b25b47a86193e 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_04_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_04_plan.json
@@ -418,16 +418,7 @@
                 }
               },
               "groupings": [{
-                "groupingExpressions": [{
-                  "selection": {
-                    "directReference": {
-                      "structField": {
-                      }
-                    },
-                    "rootReference": {
-                    }
-                  }
-                }]
+                "expressionReferences": [0]
               }],
               "measures": [{
                 "measure": {
@@ -440,6 +431,16 @@
                   },
                   "invocation": "AGGREGATION_INVOCATION_ALL"
                 }
+              }],
+              "groupingExpressions": [{
+                "selection": {
+                  "directReference": {
+                    "structField": {
+                    }
+                  },
+                  "rootReference": {
+                  }
+                }
               }]
             }
           },
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_05_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_05_plan.json
index d42975d3326d8..791cdfd367ff0 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_05_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_05_plan.json
@@ -850,16 +850,7 @@
                 }
               },
               "groupings": [{
-                "groupingExpressions": [{
-                  "selection": {
-                    "directReference": {
-                      "structField": {
-                      }
-                    },
-                    "rootReference": {
-                    }
-                  }
-                }]
+                "expressionReferences": [0]
               }],
               "measures": [{
                 "measure": {
@@ -887,6 +878,16 @@
                     }
                   }]
                 }
+              }],
+              "groupingExpressions": [{
+                "selection": {
+                  "directReference": {
+                    "structField": {
+                    }
+                  },
+                  "rootReference": {
+                  }
+                }
               }]
             }
           },
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_07_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_07_plan.json
index 82740fb3d87bd..62e385af3878f 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_07_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_07_plan.json
@@ -988,36 +988,7 @@
                 }
               },
               "groupings": [{
-                "groupingExpressions": [{
-                  "selection": {
-                    "directReference": {
-                      "structField": {
-                      }
-                    },
-                    "rootReference": {
-                    }
-                  }
-                }, {
-                  "selection": {
-                    "directReference": {
-                      "structField": {
-                        "field": 1
-                      }
-                    },
-                    "rootReference": {
-                    }
-                  }
-                }, {
-                  "selection": {
-                    "directReference": {
-                      "structField": {
-                        "field": 2
-                      }
-                    },
-                    "rootReference": {
-                    }
-                  }
-                }]
+                "expressionReferences": [0, 1, 2]
               }],
               "measures": [{
                 "measure": {
@@ -1045,6 +1016,36 @@
                     }
                   }]
                 }
+              }],
+              "groupingExpressions": [{
+                "selection": {
+                  "directReference": {
+                    "structField": {
+                    }
+                  },
+                  "rootReference": {
+                  }
+                }
+              }, {
+                "selection": {
+                  "directReference": {
+                    "structField": {
+                      "field": 1
+                    }
+                  },
+                  "rootReference": {
+                  }
+                }
+              }, {
+                "selection": {
+                  "directReference": {
+                    "structField": {
+                      "field": 2
+                    }
+                  },
+                  "rootReference": {
+                  }
+                }
               }]
             }
           },
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_08_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_08_plan.json
index 8c886f84ed166..cd53224b51159 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_08_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_08_plan.json
@@ -1167,16 +1167,7 @@
                     }
                   },
                   "groupings": [{
-                    "groupingExpressions": [{
-                      "selection": {
-                        "directReference": {
-                          "structField": {
-                          }
-                        },
-                        "rootReference": {
-                        }
-                      }
-                    }]
+                    "expressionReferences": [0]
                   }],
                   "measures": [{
                     "measure": {
@@ -1230,6 +1221,16 @@
                         }
                       }]
                     }
+                  }],
+                  "groupingExpressions": [{
+                    "selection": {
+                      "directReference": {
+                        "structField": {
+                        }
+                      },
+                      "rootReference": {
+                      }
+                    }
                   }]
                 }
               },
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_09_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_09_plan.json
index 04b367a0b5bfe..6d54d90ae2a17 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_09_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_09_plan.json
@@ -873,26 +873,7 @@
                 }
               },
               "groupings": [{
-                "groupingExpressions": [{
-                  "selection": {
-                    "directReference": {
-                      "structField": {
-                      }
-                    },
-                    "rootReference": {
-                    }
-                  }
-                }, {
-                  "selection": {
-                    "directReference": {
-                      "structField": {
-                        "field": 1
-                      }
-                    },
-                    "rootReference": {
-                    }
-                  }
-                }]
+                "expressionReferences": [0, 1]
               }],
               "measures": [{
                 "measure": {
@@ -920,6 +901,26 @@
                     }
                   }]
                 }
+              }],
+              "groupingExpressions": [{
+                "selection": {
+                  "directReference": {
+                    "structField": {
+                    }
+                  },
+                  "rootReference": {
+                  }
+                }
+              }, {
+                "selection": {
+                  "directReference": {
+                    "structField": {
+                      "field": 1
+                    }
+                  },
+                  "rootReference": {
+                  }
+                }
               }]
             }
           },
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_10_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_10_plan.json
index 2daa1dabb4238..a9265f981f263 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_10_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_10_plan.json
@@ -720,76 +720,7 @@
                         }
                       },
                       "groupings": [{
-                        "groupingExpressions": [{
-                          "selection": {
-                            "directReference": {
-                              "structField": {
-                              }
-                            },
-                            "rootReference": {
-                            }
-                          }
-                        }, {
-                          "selection": {
-                            "directReference": {
-                              "structField": {
-                                "field": 1
-                              }
-                            },
-                            "rootReference": {
-                            }
-                          }
-                        }, {
-                          "selection": {
-                            "directReference": {
-                              "structField": {
-                                "field": 2
-                              }
-                            },
-                            "rootReference": {
-                            }
-                          }
-                        }, {
-                          "selection": {
-                            "directReference": {
-                              "structField": {
-                                "field": 3
-                              }
-                            },
-                            "rootReference": {
-                            }
-                          }
-                        }, {
-                          "selection": {
-                            "directReference": {
-                              "structField": {
-                                "field": 4
-                              }
-                            },
-                            "rootReference": {
-                            }
-                          }
-                        }, {
-                          "selection": {
-                            "directReference": {
-                              "structField": {
-                                "field": 5
-                              }
-                            },
-                            "rootReference": {
-                            }
-                          }
-                        }, {
-                          "selection": {
-                            "directReference": {
-                              "structField": {
-                                "field": 6
-                              }
-                            },
-                            "rootReference": {
-                            }
-                          }
-                        }]
+                        "expressionReferences": [0, 1, 2, 3, 4, 5, 6]
                       }],
                       "measures": [{
                         "measure": {
@@ -817,6 +748,76 @@
                             }
                           }]
                         }
+                      }],
+                      "groupingExpressions": [{
+                        "selection": {
+                          "directReference": {
+                            "structField": {
+                            }
+                          },
+                          "rootReference": {
+                          }
+                        }
+                      }, {
+                        "selection": {
+                          "directReference": {
+                            "structField": {
+                              "field": 1
+                            }
+                          },
+                          "rootReference": {
+                          }
+                        }
+                      }, {
+                        "selection": {
+                          "directReference": {
+                            "structField": {
+                              "field": 2
+                            }
+                          },
+                          "rootReference": {
+                          }
+                        }
+                      }, {
+                        "selection": {
+                          "directReference": {
+                            "structField": {
+                              "field": 3
+                            }
+                          },
+                          "rootReference": {
+                          }
+                        }
+                      }, {
+                        "selection": {
+                          "directReference": {
+                            "structField": {
+                              "field": 4
+                            }
+                          },
+                          "rootReference": {
+                          }
+                        }
+                      }, {
+                        "selection": {
+                          "directReference": {
+                            "structField": {
+                              "field": 5
+                            }
+                          },
+                          "rootReference": {
+                          }
+                        }
+                      }, {
+                        "selection": {
+                          "directReference": {
+                            "structField": {
+                              "field": 6
+                            }
+                          },
+                          "rootReference": {
+                          }
+                        }
                       }]
                     }
                   },
@@ -918,7 +919,11 @@
               }]
             }
           },
-          "count": "20"
+          "countExpr": {
+            "literal": {
+              "i64": "20"
+            }
+          }
         }
       },
       "names": ["C_CUSTKEY", "C_NAME", "REVENUE", "C_ACCTBAL", "N_NAME", "C_ADDRESS", "C_PHONE", "C_COMMENT"]
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_11_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_11_plan.json
index d79b065403d54..8434543e26563 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_11_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_11_plan.json
@@ -384,16 +384,7 @@
                     }
                   },
                   "groupings": [{
-                    "groupingExpressions": [{
-                      "selection": {
-                        "directReference": {
-                          "structField": {
-                          }
-                        },
-                        "rootReference": {
-                        }
-                      }
-                    }]
+                    "expressionReferences": [0]
                   }],
                   "measures": [{
                     "measure": {
@@ -421,6 +412,16 @@
                         }
                       }]
                     }
+                  }],
+                  "groupingExpressions": [{
+                    "selection": {
+                      "directReference": {
+                        "structField": {
+                        }
+                      },
+                      "rootReference": {
+                      }
+                    }
                   }]
                 }
               },
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_12_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_12_plan.json
index db3100052704c..abd112f405794 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_12_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_12_plan.json
@@ -711,16 +711,7 @@
                 }
               },
               "groupings": [{
-                "groupingExpressions": [{
-                  "selection": {
-                    "directReference": {
-                      "structField": {
-                      }
-                    },
-                    "rootReference": {
-                    }
-                  }
-                }]
+                "expressionReferences": [0]
               }],
               "measures": [{
                 "measure": {
@@ -770,6 +761,16 @@
                     }
                   }]
                 }
+              }],
+              "groupingExpressions": [{
+                "selection": {
+                  "directReference": {
+                    "structField": {
+                    }
+                  },
+                  "rootReference": {
+                  }
+                }
               }]
             }
           },
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_13_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_13_plan.json
index 19b80b0aac73a..e73087b69cee2 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_13_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_13_plan.json
@@ -326,16 +326,7 @@
                             }
                           },
                           "groupings": [{
-                            "groupingExpressions": [{
-                              "selection": {
-                                "directReference": {
-                                  "structField": {
-                                  }
-                                },
-                                "rootReference": {
-                                }
-                              }
-                            }]
+                            "expressionReferences": [0]
                           }],
                           "measures": [{
                             "measure": {
@@ -361,6 +352,16 @@
                                 }
                               }]
                             }
+                          }],
+                          "groupingExpressions": [{
+                            "selection": {
+                              "directReference": {
+                                "structField": {
+                                }
+                              },
+                              "rootReference": {
+                              }
+                            }
                           }]
                         }
                       },
@@ -378,16 +379,7 @@
                     }
                   },
                   "groupings": [{
-                    "groupingExpressions": [{
-                      "selection": {
-                        "directReference": {
-                          "structField": {
-                          }
-                        },
-                        "rootReference": {
-                        }
-                      }
-                    }]
+                    "expressionReferences": [0]
                   }],
                   "measures": [{
                     "measure": {
@@ -400,6 +392,16 @@
                       },
                       "invocation": "AGGREGATION_INVOCATION_ALL"
                     }
+                  }],
+                  "groupingExpressions": [{
+                    "selection": {
+                      "directReference": {
+                        "structField": {
+                        }
+                      },
+                      "rootReference": {
+                      }
+                    }
                   }]
                 }
               },
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_16_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_16_plan.json
index bf97fb9185711..138bc91097c75 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_16_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_16_plan.json
@@ -754,36 +754,7 @@
                 }
               },
               "groupings": [{
-                "groupingExpressions": [{
-                  "selection": {
-                    "directReference": {
-                      "structField": {
-                      }
-                    },
-                    "rootReference": {
-                    }
-                  }
-                }, {
-                  "selection": {
-                    "directReference": {
-                      "structField": {
-                        "field": 1
-                      }
-                    },
-                    "rootReference": {
-                    }
-                  }
-                }, {
-                  "selection": {
-                    "directReference": {
-                      "structField": {
-                        "field": 2
-                      }
-                    },
-                    "rootReference": {
-                    }
-                  }
-                }]
+                "expressionReferences": [0, 1, 2]
               }],
               "measures": [{
                 "measure": {
@@ -809,6 +780,36 @@
                     }
                   }]
                 }
+              }],
+              "groupingExpressions": [{
+                "selection": {
+                  "directReference": {
+                    "structField": {
+                    }
+                  },
+                  "rootReference": {
+                  }
+                }
+              }, {
+                "selection": {
+                  "directReference": {
+                    "structField": {
+                      "field": 1
+                    }
+                  },
+                  "rootReference": {
+                  }
+                }
+              }, {
+                "selection": {
+                  "directReference": {
+                    "structField": {
+                      "field": 2
+                    }
+                  },
+                  "rootReference": {
+                  }
+                }
               }]
             }
           },
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_18_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_18_plan.json
index 7f0ff438db78e..a6455b458ee29 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_18_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_18_plan.json
@@ -441,16 +441,7 @@
                                                     }
                                                   },
                                                   "groupings": [{
-                                                    "groupingExpressions": [{
-                                                      "selection": {
-                                                        "directReference": {
-                                                          "structField": {
-                                                          }
-                                                        },
-                                                        "rootReference": {
-                                                        }
-                                                      }
-                                                    }]
+                                                    "expressionReferences": [0]
                                                   }],
                                                   "measures": [{
                                                     "measure": {
@@ -478,6 +469,16 @@
                                                         }
                                                       }]
                                                     }
+                                                  }],
+                                                  "groupingExpressions": [{
+                                                    "selection": {
+                                                      "directReference": {
+                                                        "structField": {
+                                                        }
+                                                      },
+                                                      "rootReference": {
+                                                      }
+                                                    }
                                                   }]
                                                 }
                                               },
@@ -678,56 +679,7 @@
                     }
                   },
                   "groupings": [{
-                    "groupingExpressions": [{
-                      "selection": {
-                        "directReference": {
-                          "structField": {
-                          }
-                        },
-                        "rootReference": {
-                        }
-                      }
-                    }, {
-                      "selection": {
-                        "directReference": {
-                          "structField": {
-                            "field": 1
-                          }
-                        },
-                        "rootReference": {
-                        }
-                      }
-                    }, {
-                      "selection": {
-                        "directReference": {
-                          "structField": {
-                            "field": 2
-                          }
-                        },
-                        "rootReference": {
-                        }
-                      }
-                    }, {
-                      "selection": {
-                        "directReference": {
-                          "structField": {
-                            "field": 3
-                          }
-                        },
-                        "rootReference": {
-                        }
-                      }
-                    }, {
-                      "selection": {
-                        "directReference": {
-                          "structField": {
-                            "field": 4
-                          }
-                        },
-                        "rootReference": {
-                        }
-                      }
-                    }]
+                    "expressionReferences": [0, 1, 2, 3, 4]
                   }],
                   "measures": [{
                     "measure": {
@@ -755,6 +707,56 @@
                         }
                       }]
                     }
+                  }],
+                  "groupingExpressions": [{
+                    "selection": {
+                      "directReference": {
+                        "structField": {
+                        }
+                      },
+                      "rootReference": {
+                      }
+                    }
+                  }, {
+                    "selection": {
+                      "directReference": {
+                        "structField": {
+                          "field": 1
+                        }
+                      },
+                      "rootReference": {
+                      }
+                    }
+                  }, {
+                    "selection": {
+                      "directReference": {
+                        "structField": {
+                          "field": 2
+                        }
+                      },
+                      "rootReference": {
+                      }
+                    }
+                  }, {
+                    "selection": {
+                      "directReference": {
+                        "structField": {
+                          "field": 3
+                        }
+                      },
+                      "rootReference": {
+                      }
+                    }
+                  }, {
+                    "selection": {
+                      "directReference": {
+                        "structField": {
+                          "field": 4
+                        }
+                      },
+                      "rootReference": {
+                      }
+                    }
                   }]
                 }
               },
@@ -787,7 +789,11 @@
               }]
             }
           },
-          "count": "100"
+          "countExpr": {
+            "literal": {
+              "i64": "100"
+            }
+          }
         }
       },
       "names": ["C_NAME", "C_CUSTKEY", "O_ORDERKEY", "O_ORDERDATE", "O_TOTALPRICE", "EXPR$5"]
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_21_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_21_plan.json
index c3d4fc3bcb873..9d4b1dab24c54 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_21_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_21_plan.json
@@ -988,16 +988,7 @@
                     }
                   },
                   "groupings": [{
-                    "groupingExpressions": [{
-                      "selection": {
-                        "directReference": {
-                          "structField": {
-                          }
-                        },
-                        "rootReference": {
-                        }
-                      }
-                    }]
+                    "expressionReferences": [0]
                   }],
                   "measures": [{
                     "measure": {
@@ -1010,6 +1001,16 @@
                       },
                       "invocation": "AGGREGATION_INVOCATION_ALL"
                     }
+                  }],
+                  "groupingExpressions": [{
+                    "selection": {
+                      "directReference": {
+                        "structField": {
+                        }
+                      },
+                      "rootReference": {
+                      }
+                    }
                   }]
                 }
               },
@@ -1041,7 +1042,11 @@
               }]
             }
           },
-          "count": "100"
+          "countExpr": {
+            "literal": {
+              "i64": "100"
+            }
+          }
         }
       },
       "names": ["S_NAME", "NUMWAIT"]
diff --git a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_22_plan.json b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_22_plan.json
index fcd61b23ae2de..e1bcc23bfdba6 100644
--- a/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_22_plan.json
+++ b/datafusion/substrait/tests/testdata/tpch_substrait_plans/query_22_plan.json
@@ -1438,16 +1438,7 @@
                 }
               },
               "groupings": [{
-                "groupingExpressions": [{
-                  "selection": {
-                    "directReference": {
-                      "structField": {
-                      }
-                    },
-                    "rootReference": {
-                    }
-                  }
-                }]
+                "expressionReferences": [0]
               }],
               "measures": [{
                 "measure": {
@@ -1486,6 +1477,16 @@
                     }
                   }]
                 }
+              }],
+              "groupingExpressions": [{
+                "selection": {
+                  "directReference": {
+                    "structField": {
+                    }
+                  },
+                  "rootReference": {
+                  }
+                }
               }]
             }
           },
diff --git a/datafusion/substrait/tests/utils.rs b/datafusion/substrait/tests/utils.rs
index 89363931f1594..1e1f3fec1b569 100644
--- a/datafusion/substrait/tests/utils.rs
+++ b/datafusion/substrait/tests/utils.rs
@@ -157,7 +157,6 @@ pub mod test {
             Ok(())
         }
 
-        #[expect(deprecated)]
         fn collect_schemas_from_rel(&mut self, rel: &Rel) -> Result<()> {
             let rel_type = rel
                 .rel_type
@@ -195,10 +194,8 @@ pub mod test {
                 }
                 RelType::Aggregate(a) => {
                     self.apply(a.input.as_ref().map(|b| b.as_ref()))?;
-                    for grouping in a.groupings.iter() {
-                        for expr in grouping.grouping_expressions.iter() {
-                            self.collect_schemas_from_expr(expr)?
-                        }
+                    for expr in a.grouping_expressions.iter() {
+                        self.collect_schemas_from_expr(expr)?
                     }
                     for measure in a.measures.iter() {
                         if let Some(agg_fn) = measure.measure.as_ref() {
@@ -483,9 +480,7 @@ pub mod test {
                     }
                 }
                 RexType::DynamicParameter(_) => {}
-                // Enum is deprecated
-                #[expect(deprecated)]
-                RexType::Enum(_) => {}
+                RexType::ExecutionContextVariable(_) => {}
                 RexType::Lambda(_) | RexType::LambdaInvocation(_) => {}
             }
             Ok(())