diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/BeamAdapterUtils.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/BeamAdapterUtils.java
index 065796057c23..46e91c7598a0 100644
--- a/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/BeamAdapterUtils.java
+++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/BeamAdapterUtils.java
@@ -35,6 +35,7 @@
 import org.apache.beam.sdk.values.PCollectionTuple;
 import org.apache.beam.sdk.values.PInput;
 import org.apache.beam.sdk.values.POutput;
+import org.apache.beam.vendor.guava.v32_1_2_jre.com.google.common.base.Preconditions;
 import org.apache.beam.vendor.guava.v32_1_2_jre.com.google.common.collect.ImmutableMap;
 import org.apache.beam.vendor.guava.v32_1_2_jre.com.google.common.collect.Maps;
 import org.apache.flink.api.common.typeinfo.TypeInformation;
@@ -50,7 +51,7 @@ Map<String, DataSetOrStreamT> translate(
         ExecutionEnvironment executionEnvironment);
   }
 
-  @SuppressWarnings({"nullness", "rawtypes"})
+  @SuppressWarnings({"rawtypes"})
   static <DataSetOrStreamT, BeamInputT extends PInput, BeamOutputT extends POutput>
       Map<String, DataSetOrStreamT> applyBeamPTransformInternal(
           Map<String, ? extends DataSetOrStreamT> inputs,
@@ -75,7 +76,8 @@ Map<String, DataSetOrStreamT> applyBeamPTransformInternal(
                         new FlinkInput<>(
                             key,
                             BeamAdapterCoderUtils.typeInformationToCoder(
-                                getTypeInformation.apply(flinkInput), coderRegistry)))));
+                                getTypeInformation.apply(Preconditions.checkNotNull(flinkInput)),
+                                coderRegistry)))));
 
     // Actually apply the transform to create Beam outputs.
     Map<String, PCollection<?>> beamOutputs =
diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/BeamFlinkDataSetAdapter.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/BeamFlinkDataSetAdapter.java
index 93b3a8492a67..f3e20f3d9a94 100644
--- a/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/BeamFlinkDataSetAdapter.java
+++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/BeamFlinkDataSetAdapter.java
@@ -31,6 +31,7 @@
 import org.apache.beam.sdk.options.PipelineOptions;
 import org.apache.beam.sdk.options.PipelineOptionsFactory;
 import org.apache.beam.sdk.transforms.PTransform;
+import org.apache.beam.sdk.util.Preconditions;
 import org.apache.beam.sdk.util.WindowedValue;
 import org.apache.beam.sdk.util.construction.PipelineOptionsTranslation;
 import org.apache.beam.sdk.util.construction.graph.PipelineNode;
@@ -59,55 +60,54 @@ public BeamFlinkDataSetAdapter(PipelineOptions pipelineOptions) {
     this.pipelineOptions = pipelineOptions;
   }
 
-  @SuppressWarnings("nullness")
   public <InputT, OutputT, CollectionT extends PCollection<? extends InputT>>
       DataSet<OutputT> applyBeamPTransform(
           DataSet<InputT> input, PTransform<CollectionT, PCollection<OutputT>> transform) {
     return (DataSet)
-        this.<CollectionT, PCollection<OutputT>>applyBeamPTransformInternal(
+        getNonNull(
+            applyBeamPTransformInternal(
                 ImmutableMap.of("input", input),
-                (pipeline, map) -> (CollectionT) map.get("input"),
+                (pipeline, map) -> (CollectionT) getNonNull(map, "input"),
                 (output) -> ImmutableMap.of("output", output),
                 transform,
-                input.getExecutionEnvironment())
-            .get("output");
+                input.getExecutionEnvironment()),
+            "output");
   }
 
-  @SuppressWarnings("nullness")
   public <OutputT> DataSet<OutputT> applyBeamPTransform(
       Map<String, ? extends DataSet<?>> inputs,
       PTransform<PCollectionTuple, PCollection<OutputT>> transform) {
     return (DataSet)
-        applyBeamPTransformInternal(
+        getNonNull(
+            applyBeamPTransformInternal(
                 inputs,
                 BeamAdapterUtils::mapToTuple,
                 (output) -> ImmutableMap.of("output", output),
                 transform,
-                inputs.values().stream().findAny().get().getExecutionEnvironment())
-            .get("output");
+                inputs.values().stream().findAny().get().getExecutionEnvironment()),
+            "output");
   }
 
-  @SuppressWarnings("nullness")
   public <OutputT> DataSet<OutputT> applyBeamPTransform(
       ExecutionEnvironment executionEnvironment,
       PTransform<PBegin, PCollection<OutputT>> transform) {
     return (DataSet)
-        applyBeamPTransformInternal(
+        getNonNull(
+            applyBeamPTransformInternal(
                 ImmutableMap.<String, DataSet<?>>of(),
                 (pipeline, map) -> PBegin.in(pipeline),
                 (output) -> ImmutableMap.of("output", output),
                 transform,
-                executionEnvironment)
-            .get("output");
+                executionEnvironment),
+            "output");
   }
 
-  @SuppressWarnings("nullness")
   public <InputT, CollectionT extends PCollection<? extends InputT>>
       Map<String, DataSet<?>> applyMultiOutputBeamPTransform(
           DataSet<InputT> input, PTransform<CollectionT, PCollectionTuple> transform) {
     return applyBeamPTransformInternal(
         ImmutableMap.of("input", input),
-        (pipeline, map) -> (CollectionT) map.get("input"),
+        (pipeline, map) -> (CollectionT) getNonNull(map, "input"),
         BeamAdapterUtils::tupleToMap,
         transform,
         input.getExecutionEnvironment());
@@ -134,13 +134,12 @@ public Map<String, DataSet<?>> applyMultiOutputBeamPTransform(
         executionEnvironment);
   }
 
-  @SuppressWarnings("nullness")
   public <InputT, CollectionT extends PCollection<? extends InputT>>
       void applyNoOutputBeamPTransform(
           DataSet<InputT> input, PTransform<CollectionT, PDone> transform) {
     applyBeamPTransformInternal(
         ImmutableMap.of("input", input),
-        (pipeline, map) -> (CollectionT) map.get("input"),
+        (pipeline, map) -> (CollectionT) getNonNull(map, "input"),
         pDone -> ImmutableMap.of(),
         transform,
         input.getExecutionEnvironment());
@@ -217,11 +216,11 @@ private <InputT> FlinkBatchPortablePipelineTranslator.PTransformTranslator flink
       // When we run into a FlinkInput operator, it "produces" the corresponding input as its
       // "computed result."
       String inputId = t.getTransform().getSpec().getPayload().toStringUtf8();
-      DataSet<InputT> flinkInput = (DataSet<InputT>) inputMap.get(inputId);
-      // To make the nullness checker happy...
-      if (flinkInput == null) {
-        throw new IllegalStateException("Missing input: " + inputId);
-      }
+      DataSet<InputT> flinkInput =
+          org.apache.beam.sdk.util.Preconditions.checkStateNotNull(
+              (DataSet<InputT>) inputMap.get(inputId),
+              "missing input referenced in proto: ",
+              inputId);
       context.addDataSet(
           Iterables.getOnlyElement(t.getTransform().getOutputsMap().values()),
           // new MapOperator(...) rather than .map to manually designate the type information.
@@ -262,4 +261,8 @@ private <InputT> FlinkBatchPortablePipelineTranslator.PTransformTranslator flink
               "StripWindows"));
     };
   }
+
+  private <K, V> V getNonNull(Map<K, V> map, K key) {
+    return Preconditions.checkStateNotNull(map.get(Preconditions.checkArgumentNotNull(key)));
+  }
 }
diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/FlinkInput.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/FlinkInput.java
index 0b76319e9eac..7ee261ca4b5f 100644
--- a/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/FlinkInput.java
+++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/FlinkInput.java
@@ -61,7 +61,6 @@ public PCollection<T> expand(PBegin input) {
   }
 
   // This Translator translates this kind of PTransform into a Beam proto representation.
-  @SuppressWarnings("nullness")
   @AutoService(TransformPayloadTranslatorRegistrar.class)
   public static class Translator
       implements PTransformTranslation.TransformPayloadTranslator<FlinkInput<?>>,
@@ -72,6 +71,7 @@ public String getUrn() {
     }
 
     @Override
+    @SuppressWarnings("nullness") // TODO(https://github.com/apache/beam/issues/20497)
     public RunnerApi.FunctionSpec translate(
         AppliedPTransform<?, ?, FlinkInput<?>> application, SdkComponents components)
         throws IOException {
diff --git a/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/FlinkOutput.java b/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/FlinkOutput.java
index 2cc25236c1c3..64577901765d 100644
--- a/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/FlinkOutput.java
+++ b/runners/flink/src/main/java/org/apache/beam/runners/flink/adapter/FlinkOutput.java
@@ -52,7 +52,6 @@ public PDone expand(PCollection<T> input) {
     return PDone.in(input.getPipeline());
   }
 
-  @SuppressWarnings("nullness")
   @AutoService(TransformPayloadTranslatorRegistrar.class)
   public static class Translator
       implements PTransformTranslation.TransformPayloadTranslator<FlinkOutput<?>>,
@@ -63,6 +62,7 @@ public String getUrn() {
     }
 
     @Override
+    @SuppressWarnings("nullness") // TODO(https://github.com/apache/beam/issues/20497)
     public RunnerApi.FunctionSpec translate(
         AppliedPTransform<?, ?, FlinkOutput<?>> application, SdkComponents components)
         throws IOException {