diff --git a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/reflect/DoFnSignatures.java b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/reflect/DoFnSignatures.java
index 310736c014cc..bda1beb2b71c 100644
--- a/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/reflect/DoFnSignatures.java
+++ b/sdks/java/core/src/main/java/org/apache/beam/sdk/transforms/reflect/DoFnSignatures.java
@@ -104,6 +104,8 @@
 import org.apache.beam.vendor.guava.v32_1_2_jre.com.google.common.collect.Maps;
 import org.checkerframework.checker.nullness.qual.Nullable;
 import org.joda.time.Instant;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /** Utilities for working with {@link DoFnSignature}. See {@link #getSignature}. */
 @Internal
@@ -113,6 +115,8 @@
 })
 public class DoFnSignatures {
 
+  private static final Logger LOG = LoggerFactory.getLogger(DoFnSignatures.class);
+
   private DoFnSignatures() {}
 
   /**
@@ -2327,12 +2331,77 @@ private static Map<String, DoFnSignature.StateDeclaration> analyzeStateDeclarati
           (TypeDescriptor<? extends State>)
               TypeDescriptor.of(fnClazz).resolveType(unresolvedStateType);
 
+      // Warn if ValueState contains a collection type that could benefit from specialized state
+      warnIfValueStateContainsCollection(fnClazz, id, stateType);
+
       declarations.put(id, DoFnSignature.StateDeclaration.create(id, field, stateType));
     }
 
     return ImmutableMap.copyOf(declarations);
   }
 
+  /**
+   * Warns if a ValueState is declared with a collection type (Map, List, Set) that could benefit
+   * from using specialized state types (MapState, BagState, SetState) for better performance.
+   */
+  private static void warnIfValueStateContainsCollection(
+      Class<?> fnClazz, String stateId, TypeDescriptor<? extends State> stateType) {
+    if (!stateType.isSubtypeOf(TypeDescriptor.of(ValueState.class))) {
+      return;
+    }
+
+    try {
+      // Get the type directly and extract ValueState's type parameter
+      Type type = stateType.getType();
+      if (!(type instanceof ParameterizedType)) {
+        return;
+      }
+
+      // Find ValueState in the type hierarchy and get its type argument
+      Type valueType = null;
+      ParameterizedType pType = (ParameterizedType) type;
+      if (pType.getRawType() == ValueState.class) {
+        valueType = pType.getActualTypeArguments()[0];
+      } else {
+        // For subtypes of ValueState, we need to resolve the type parameter
+        return;
+      }
+
+      if (valueType == null
+          || valueType instanceof java.lang.reflect.TypeVariable
+          || valueType instanceof java.lang.reflect.WildcardType) {
+        // Cannot determine actual type, skip warning
+        return;
+      }
+
+      TypeDescriptor<?> valueTypeDescriptor = TypeDescriptor.of(valueType);
+      Class<?> rawType = valueTypeDescriptor.getRawType();
+
+      String recommendation = null;
+      if (Map.class.isAssignableFrom(rawType)) {
+        recommendation = "MapState";
+      } else if (List.class.isAssignableFrom(rawType)) {
+        recommendation = "BagState or OrderedListState";
+      } else if (java.util.Set.class.isAssignableFrom(rawType)) {
+        recommendation = "SetState";
+      }
+
+      if (recommendation != null) {
+        LOG.warn(
+            "DoFn {} declares ValueState '{}' with type {}. "
+                + "Storing collections in ValueState requires reading and writing the entire "
+                + "collection on each access, which can cause performance issues. "
+                + "Consider using {} instead for better performance with large collections.",
+            fnClazz.getSimpleName(),
+            stateId,
+            rawType.getSimpleName(),
+            recommendation);
+      }
+    } catch (Exception e) {
+      // If we can't determine the type, don't warn - it's just an optimization hint
+    }
+  }
+
   private static @Nullable Method findAnnotatedMethod(
       ErrorReporter errors, Class<? extends Annotation> anno, Class<?> fnClazz, boolean required) {
     Collection<Method> matches =
diff --git a/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/reflect/DoFnSignaturesTest.java b/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/reflect/DoFnSignaturesTest.java
index de4a622e03d7..a394b23cd7a0 100644
--- a/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/reflect/DoFnSignaturesTest.java
+++ b/sdks/java/core/src/test/java/org/apache/beam/sdk/transforms/reflect/DoFnSignaturesTest.java
@@ -1700,4 +1700,65 @@ public void onMyTimer() {}
     @Override
     public void processWithTimer(ProcessContext context, Timer timer) {}
   }
+
+  // Test DoFns for ValueState collection warning tests
+  private static class DoFnWithMapValueState extends DoFn<String, String> {
+    @StateId("mapState")
+    private final StateSpec<ValueState<java.util.Map<String, String>>> mapState =
+        StateSpecs.value();
+
+    @ProcessElement
+    public void process() {}
+  }
+
+  private static class DoFnWithListValueState extends DoFn<String, String> {
+    @StateId("listState")
+    private final StateSpec<ValueState<java.util.List<String>>> listState = StateSpecs.value();
+
+    @ProcessElement
+    public void process() {}
+  }
+
+  private static class DoFnWithSetValueState extends DoFn<String, String> {
+    @StateId("setState")
+    private final StateSpec<ValueState<java.util.Set<String>>> setState = StateSpecs.value();
+
+    @ProcessElement
+    public void process() {}
+  }
+
+  private static class DoFnWithSimpleValueState extends DoFn<String, String> {
+    @StateId("simpleState")
+    private final StateSpec<ValueState<String>> simpleState = StateSpecs.value();
+
+    @ProcessElement
+    public void process() {}
+  }
+
+  @Test
+  public void testValueStateWithMapLogsWarning() {
+    // This test verifies that the signature can be parsed for DoFns with collection ValueState.
+    // The warning is logged but doesn't prevent the signature from being created.
+    DoFnSignature signature = DoFnSignatures.getSignature(DoFnWithMapValueState.class);
+    assertThat(signature.stateDeclarations().get("mapState"), notNullValue());
+  }
+
+  @Test
+  public void testValueStateWithListLogsWarning() {
+    DoFnSignature signature = DoFnSignatures.getSignature(DoFnWithListValueState.class);
+    assertThat(signature.stateDeclarations().get("listState"), notNullValue());
+  }
+
+  @Test
+  public void testValueStateWithSetLogsWarning() {
+    DoFnSignature signature = DoFnSignatures.getSignature(DoFnWithSetValueState.class);
+    assertThat(signature.stateDeclarations().get("setState"), notNullValue());
+  }
+
+  @Test
+  public void testValueStateWithSimpleTypeNoWarning() {
+    // Simple types should not trigger any warning
+    DoFnSignature signature = DoFnSignatures.getSignature(DoFnWithSimpleValueState.class);
+    assertThat(signature.stateDeclarations().get("simpleState"), notNullValue());
+  }
 }
diff --git a/sdks/java/io/iceberg/src/main/java/org/apache/beam/sdk/io/iceberg/IcebergScanConfig.java b/sdks/java/io/iceberg/src/main/java/org/apache/beam/sdk/io/iceberg/IcebergScanConfig.java
index 3829baa43665..011d17c06579 100644
--- a/sdks/java/io/iceberg/src/main/java/org/apache/beam/sdk/io/iceberg/IcebergScanConfig.java
+++ b/sdks/java/io/iceberg/src/main/java/org/apache/beam/sdk/io/iceberg/IcebergScanConfig.java
@@ -93,10 +93,29 @@ static org.apache.iceberg.Schema resolveSchema(
     if (keep != null && !keep.isEmpty()) {
       selectedFieldsBuilder.addAll(keep);
     } else if (drop != null && !drop.isEmpty()) {
-      Set<String> fields =
-          schema.columns().stream().map(Types.NestedField::name).collect(Collectors.toSet());
-      drop.forEach(fields::remove);
-      selectedFieldsBuilder.addAll(fields);
+      // Get all field paths including nested ones
+      java.util.List<String> allPaths = new java.util.ArrayList<>(
+          org.apache.iceberg.types.TypeUtil.indexByName(schema.asStruct()).keySet());
+      java.util.Collections.sort(allPaths);
+
+      // Identify leaf fields only (fields that are not parents of other fields)
+      // This prevents selecting a parent struct from implicitly including dropped children
+      java.util.Set<String> leaves = new java.util.HashSet<>();
+      for (int i = 0; i < allPaths.size(); i++) {
+        String path = allPaths.get(i);
+        // If the next path starts with "path.", then "path" is a parent - skip it
+        if (i + 1 < allPaths.size() && allPaths.get(i + 1).startsWith(path + ".")) {
+          continue;
+        }
+        leaves.add(path);
+      }
+
+      // Remove fields that are dropped or are children of dropped fields
+      for (String d : drop) {
+        leaves.removeIf(f -> f.equals(d) || f.startsWith(d + "."));
+      }
+
+      selectedFieldsBuilder.addAll(leaves);
     } else {
       // default: include all columns
       return schema;
@@ -327,7 +346,9 @@ void validate(Table table) {
         param = "drop";
         fieldsSpecified = newHashSet(checkNotNull(drop));
       }
-      table.schema().columns().forEach(nf -> fieldsSpecified.remove(nf.name()));
+      // Use findField() to support nested column paths (e.g., "colA.colB")
+      // Iceberg's Schema.findField() resolves dot-notation paths for nested fields
+      fieldsSpecified.removeIf(name -> table.schema().findField(name) != null);
 
       checkArgument(
           fieldsSpecified.isEmpty(),
diff --git a/sdks/java/io/iceberg/src/test/java/org/apache/beam/sdk/io/iceberg/IcebergIOReadTest.java b/sdks/java/io/iceberg/src/test/java/org/apache/beam/sdk/io/iceberg/IcebergIOReadTest.java
index bb303ea9c305..6e823cb894bf 100644
--- a/sdks/java/io/iceberg/src/test/java/org/apache/beam/sdk/io/iceberg/IcebergIOReadTest.java
+++ b/sdks/java/io/iceberg/src/test/java/org/apache/beam/sdk/io/iceberg/IcebergIOReadTest.java
@@ -273,6 +273,55 @@ public void testProjectedSchema() {
     assertTrue(projectKeep.sameSchema(expectedKeep));
   }
 
+  @Test
+  public void testNestedColumnPruningValidation() {
+    // Test that nested column paths (dot notation) are accepted in keep/drop configuration
+    org.apache.iceberg.Schema schemaWithNested =
+        new org.apache.iceberg.Schema(
+            required(1, "id", StringType.get()),
+            required(
+                2,
+                "data",
+                StructType.of(
+                    required(3, "name", StringType.get()),
+                    required(4, "value", StringType.get()))),
+            required(5, "metadata", StringType.get()));
+
+    // Test that nested column path "data.name" is valid and can be selected
+    org.apache.iceberg.Schema projectNestedKeep =
+        resolveSchema(schemaWithNested, asList("id", "data.name"), null);
+
+    // Verify the projected schema contains the nested field
+    assertTrue(projectNestedKeep.findField("id") != null);
+    assertTrue(projectNestedKeep.findField("data.name") != null);
+  }
+
+  @Test
+  public void testNestedColumnDropValidation() {
+    // Test that nested column paths work correctly with drop configuration
+    org.apache.iceberg.Schema schemaWithNested =
+        new org.apache.iceberg.Schema(
+            required(1, "id", StringType.get()),
+            required(
+                2,
+                "data",
+                StructType.of(
+                    required(3, "name", StringType.get()),
+                    required(4, "value", StringType.get()))),
+            required(5, "metadata", StringType.get()));
+
+    // Test dropping a nested field "data.name" - should keep id, data.value, metadata
+    org.apache.iceberg.Schema projectNestedDrop =
+        resolveSchema(schemaWithNested, null, asList("data.name"));
+
+    // Verify "data.name" is NOT in the projected schema
+    assertTrue(projectNestedDrop.findField("id") != null);
+    assertTrue(projectNestedDrop.findField("data.value") != null);
+    assertTrue(projectNestedDrop.findField("metadata") != null);
+    // data.name should be dropped
+    assertTrue(projectNestedDrop.findField("data.name") == null);
+  }
+
   @Test
   public void testSimpleScan() throws Exception {
     TableIdentifier tableId =