diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Distinct.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Distinct.java
index 641412772bf3..852e1fb31c90 100644
--- a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Distinct.java
+++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Distinct.java
@@ -61,9 +61,6 @@
  *
  * @param <T> the type of the elements of the input and output {@code PCollection}s
  */
-@SuppressWarnings({
-  "nullness" // TODO(https://github.com/apache/beam/issues/20497)
-})
 public class Distinct<T> extends PTransform<PCollection<T>, PCollection<T>> {
 
   /**
@@ -148,10 +145,10 @@ public void processElement(
   public static class WithRepresentativeValues<T, IdT>
       extends PTransform<PCollection<T>, PCollection<T>> {
     private final SerializableFunction<T, IdT> fn;
-    private final TypeDescriptor<IdT> representativeType;
+    private final @Nullable TypeDescriptor<IdT> representativeType;
 
     private WithRepresentativeValues(
-        SerializableFunction<T, IdT> fn, TypeDescriptor<IdT> representativeType) {
+        SerializableFunction<T, IdT> fn, @Nullable TypeDescriptor<IdT> representativeType) {
       this.fn = fn;
       this.representativeType = representativeType;
     }
diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Latest.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Latest.java
index cd52f05cad5e..dc75ea9d3b0b 100644
--- a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Latest.java
+++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Latest.java
@@ -17,8 +17,8 @@
  */
 package org.apache.beam.sdk.transforms;
 
+import static org.apache.beam.sdk.util.Preconditions.checkArgumentNotNull;
 import static org.apache.beam.vendor.guava.v32_1_2_jre.com.google.common.base.Preconditions.checkArgument;
-import static org.apache.beam.vendor.guava.v32_1_2_jre.com.google.common.base.Preconditions.checkNotNull;
 import static org.apache.beam.vendor.guava.v32_1_2_jre.com.google.common.base.Preconditions.checkState;
 
 import java.util.Iterator;
@@ -31,6 +31,7 @@
 import org.apache.beam.sdk.values.PCollection;
 import org.apache.beam.sdk.values.TimestampedValue;
 import org.apache.beam.vendor.guava.v32_1_2_jre.com.google.common.annotations.VisibleForTesting;
+import org.checkerframework.checker.nullness.qual.Nullable;
 
 /**
  * {@link PTransform} and {@link Combine.CombineFn} for computing the latest element in a {@link
@@ -50,9 +51,6 @@
  *
  * <p>For elements with the same timestamp, the element chosen for output is arbitrary.
  */
-@SuppressWarnings({
-  "nullness" // TODO(https://github.com/apache/beam/issues/20497)
-})
 public class Latest {
   // Do not instantiate
   private Latest() {}
@@ -88,25 +86,37 @@ public static <K, V> PTransform<PCollection<KV<K, V>>, PCollection<KV<K, V>>> pe
   /**
    * A {@link Combine.CombineFn} that computes the latest element from a set of inputs.
    *
+   * <p>The accumulator holds a {@literal null} value until the first input arrives, so combining an
+   * empty input yields {@literal null}. {@code T} must therefore be instantiated at a nullable type
+   * for the output to be sound, which the declaration cannot say without changing the public
+   * signature of {@link Latest#combineFn()}.
+   *
    * @param <T> Type of input element.
    * @see Latest
    */
   @VisibleForTesting
-  static class LatestFn<T> extends Combine.CombineFn<TimestampedValue<T>, TimestampedValue<T>, T> {
+  static class LatestFn<T>
+      extends Combine.CombineFn<TimestampedValue<T>, TimestampedValue<@Nullable T>, T> {
     /** Construct a new {@link LatestFn} instance. */
     public LatestFn() {}
 
     @Override
-    public TimestampedValue<T> createAccumulator() {
+    public TimestampedValue<@Nullable T> createAccumulator() {
       return TimestampedValue.atMinimumTimestamp(null);
     }
 
     @Override
-    public TimestampedValue<T> addInput(
-        TimestampedValue<T> accumulator, TimestampedValue<T> input) {
-      checkNotNull(accumulator, "accumulator must be non-null");
-      checkNotNull(input, "input must be non-null");
+    public TimestampedValue<@Nullable T> addInput(
+        TimestampedValue<@Nullable T> accumulator, TimestampedValue<T> input) {
+      checkArgumentNotNull(accumulator, "accumulator must be non-null");
+      checkArgumentNotNull(input, "input must be non-null");
+
+      return latest(accumulator, input);
+    }
 
+    /** Returns whichever argument is later, preferring a non-null value when they are equal. */
+    private static <T> TimestampedValue<@Nullable T> latest(
+        TimestampedValue<@Nullable T> accumulator, TimestampedValue<@Nullable T> input) {
       if (input.getTimestamp().isBefore(accumulator.getTimestamp())) {
         return accumulator;
       } else if (input.getTimestamp().isAfter(accumulator.getTimestamp())) {
@@ -117,13 +127,15 @@ public TimestampedValue<T> addInput(
     }
 
     @Override
-    public Coder<TimestampedValue<T>> getAccumulatorCoder(
+    @SuppressWarnings("nullness") // accumulated values may be null
+    public Coder<TimestampedValue<@Nullable T>> getAccumulatorCoder(
         CoderRegistry registry, Coder<TimestampedValue<T>> inputCoder)
         throws CannotProvideCoderException {
       return NullableCoder.of(inputCoder);
     }
 
     @Override
+    @SuppressWarnings("nullness") // the output is null when the input is empty
     public Coder<T> getDefaultOutputCoder(
         CoderRegistry registry, Coder<TimestampedValue<T>> inputCoder)
         throws CannotProvideCoderException {
@@ -138,24 +150,28 @@ public Coder<T> getDefaultOutputCoder(
     }
 
     @Override
-    public TimestampedValue<T> mergeAccumulators(Iterable<TimestampedValue<T>> accumulators) {
-      checkNotNull(accumulators, "accumulators must be non-null");
+    public TimestampedValue<@Nullable T> mergeAccumulators(
+        Iterable<TimestampedValue<@Nullable T>> accumulators) {
+      checkArgumentNotNull(accumulators, "accumulators must be non-null");
 
-      Iterator<TimestampedValue<T>> iter = accumulators.iterator();
+      Iterator<TimestampedValue<@Nullable T>> iter = accumulators.iterator();
       if (!iter.hasNext()) {
         return createAccumulator();
       }
 
-      TimestampedValue<T> merged = iter.next();
+      TimestampedValue<@Nullable T> merged = iter.next();
       while (iter.hasNext()) {
-        merged = addInput(merged, iter.next());
+        TimestampedValue<@Nullable T> next = iter.next();
+        checkArgumentNotNull(next, "input must be non-null");
+        merged = latest(merged, next);
       }
 
       return merged;
     }
 
     @Override
-    public T extractOutput(TimestampedValue<T> accumulator) {
+    @SuppressWarnings("nullness") // the output is null until the first input arrives
+    public T extractOutput(TimestampedValue<@Nullable T> accumulator) {
       return accumulator.getValue();
     }
   }
@@ -178,7 +194,7 @@ private static class PerKey<K, V>
       extends PTransform<PCollection<KV<K, V>>, PCollection<KV<K, V>>> {
     @Override
     public PCollection<KV<K, V>> expand(PCollection<KV<K, V>> input) {
-      checkNotNull(input);
+      checkArgumentNotNull(input);
       checkArgument(
           input.getCoder() instanceof KvCoder,
           "Input specifiedCoder must be an instance of KvCoder, but was %s",
diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Reify.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Reify.java
index da6feef92d65..2c4f16f1227b 100644
--- a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Reify.java
+++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Reify.java
@@ -32,6 +32,7 @@
 import org.apache.beam.sdk.values.TimestampedValue.TimestampedValueCoder;
 import org.apache.beam.sdk.values.ValueInSingleWindow;
 import org.apache.beam.sdk.values.ValueKind;
+import org.checkerframework.checker.nullness.qual.Nullable;
 import org.joda.time.Duration;
 import org.joda.time.Instant;
 
@@ -39,9 +40,6 @@
  * {@link PTransform PTransforms} for converting between explicit and implicit form of various Beam
  * values.
  */
-@SuppressWarnings({
-  "nullness" // TODO(https://github.com/apache/beam/issues/20497)
-})
 public class Reify {
   private static class ReifyView<K, V> extends PTransform<PCollection<K>, PCollection<KV<K, V>>> {
     private final PCollectionView<V> view;
@@ -80,7 +78,7 @@ private ReifyViewInGlobalWindow(PCollectionView<V> view, Coder<V> coder) {
     @Override
     public PCollection<V> expand(PBegin input) {
       return input
-          .apply(Create.of((Void) null).withCoder(VoidCoder.of()))
+          .apply(Create.<@Nullable Void>of((@Nullable Void) null).withCoder(VoidCoder.of()))
           .apply(Reify.viewAsValues(view, coder))
           .apply(Values.create());
     }
diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Sample.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Sample.java
index d0017c88f6a4..a838106ff376 100644
--- a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Sample.java
+++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/Sample.java
@@ -43,10 +43,7 @@
  * <p>{@link #combineFn} can also be used manually, in combination with state and with the {@link
  * Combine} transform.
  */
-@SuppressWarnings({
-  "nullness", // TODO(https://github.com/apache/beam/issues/20497)
-  "rawtypes"
-})
+@SuppressWarnings({"rawtypes"})
 public class Sample {
 
   /** Returns a {@link CombineFn} that computes a fixed-sized uniform sample of its inputs. */
@@ -282,6 +279,7 @@ public List<T> mergeAccumulators(Iterable<List<T>> accumulators) {
     }
 
     @Override
+    @SuppressWarnings("nullness") // the output is null when the input is empty
     public T extractOutput(List<T> accumulator) {
       Iterator<T> it = internal.extractOutput(accumulator).iterator();
       return it.hasNext() ? it.next() : null;
diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/values/TimestampedValue.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/values/TimestampedValue.java
index 753ee4c2b9f8..8bcf9ffb0f28 100644
--- a/sdks/java/core/src/main/java/org/apache/beam/sdk/values/TimestampedValue.java
+++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/values/TimestampedValue.java
@@ -31,6 +31,7 @@
 import org.apache.beam.sdk.coders.StructuredCoder;
 import org.apache.beam.sdk.transforms.windowing.BoundedWindow;
 import org.checkerframework.checker.nullness.qual.Nullable;
+import org.checkerframework.framework.qual.Covariant;
 import org.joda.time.Instant;
 
 /**
@@ -41,6 +42,8 @@
  *
  * @param <V> the type of the value
  */
+// Immutable, so the value type may be widened.
+@Covariant(0)
 public class TimestampedValue<V extends @Nullable Object> {
   /**
    * Returns a new {@link TimestampedValue} with the {@link BoundedWindow#TIMESTAMP_MIN_VALUE
diff --git a/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/LatestFnTest.java b/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/LatestFnTest.java
index 3eafbaa7c862..b37f0588438f 100644
--- a/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/LatestFnTest.java
+++ b/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/LatestFnTest.java
@@ -100,14 +100,14 @@ public void testAddInputSameTimestamp() {
 
   @Test
   public void testAddInputNullAccumulator() {
-    thrown.expect(NullPointerException.class);
+    thrown.expect(IllegalArgumentException.class);
     thrown.expectMessage("accumulator");
     fn.addInput(null, TV);
   }
 
   @Test
   public void testAddInputNullInput() {
-    thrown.expect(NullPointerException.class);
+    thrown.expect(IllegalArgumentException.class);
     thrown.expectMessage("input");
     fn.addInput(TV, null);
   }
@@ -151,7 +151,7 @@ public void testMergeAccumulatorsAllDefaultAccumulators() {
 
   @Test
   public void testMergeAccumulatorsNullIterable() {
-    thrown.expect(NullPointerException.class);
+    thrown.expect(IllegalArgumentException.class);
     thrown.expectMessage("accumulators");
     fn.mergeAccumulators(null);
   }