diff --git a/sdk/src/main/java/com/google/cloud/dataflow/sdk/runners/inprocess/InMemoryWatermarkManager.java b/sdk/src/main/java/com/google/cloud/dataflow/sdk/runners/inprocess/InMemoryWatermarkManager.java
index 6f68b7e42f..918a7f4a1c 100644
--- a/sdk/src/main/java/com/google/cloud/dataflow/sdk/runners/inprocess/InMemoryWatermarkManager.java
+++ b/sdk/src/main/java/com/google/cloud/dataflow/sdk/runners/inprocess/InMemoryWatermarkManager.java
@@ -466,9 +466,6 @@ public synchronized Instant getEarliestTimerTimestamp() {
     }
 
     private synchronized void updateTimers(TimerUpdate update) {
-      for (TimerData completedTimer : update.completedTimers) {
-        pendingTimers.remove(completedTimer);
-      }
       Map<TimeDomain, NavigableSet<TimerData>> timerMap = timerMap(update.key);
       for (TimerData addedTimer : update.setTimers) {
         NavigableSet<TimerData> timerQueue = timerMap.get(addedTimer.getDomain());
@@ -476,6 +473,10 @@ private synchronized void updateTimers(TimerUpdate update) {
           timerQueue.add(addedTimer);
         }
       }
+
+      for (TimerData completedTimer : update.completedTimers) {
+        pendingTimers.remove(completedTimer);
+      }
       for (TimerData deletedTimer : update.deletedTimers) {
         NavigableSet<TimerData> timerQueue = timerMap.get(deletedTimer.getDomain());
         if (timerQueue != null) {
@@ -829,10 +830,16 @@ private void refreshWatermarks(AppliedPTransform<?, ?, ?> transform) {
   }
 
   /**
-   * Removes all of the completed Timers from the collection of pending timers, adds all new timers,
-   * and removes all deleted timers. Removes all elements consumed by the input bundle from the
-   * {@link PTransform PTransforms} collection of pending elements, and adds all elements produced
-   * by the {@link PTransform} to the pending queue of each consumer.
+   * First adds all produced elements to the queue of pending elements for each consumer, then adds
+   * all pending timers to the collection of pending timers, then removes all completed and deleted
+   * timers from the collection of pending timers, then removes all completed elements from the
+   * pending queue of the transform.
+   *
+   * <p>It is required that all newly pending elements are added to the queue of pending elements
+   * for each consumer prior to the completed elements being removed, as doing otherwise could cause
+   * a Watermark to appear in a state in which the upstream (completed) element does not hold the
+   * watermark but the element it produced is not yet pending. This can cause the watermark to
+   * erroneously advance.
    */
   private void updatePending(
       CommittedBundle<?> input,
@@ -840,17 +847,22 @@ private void updatePending(
       TimerUpdate timerUpdate,
       Iterable<? extends CommittedBundle<?>> outputs) {
     TransformWatermarks completedTransform = transformToWatermarks.get(transform);
-    completedTransform.updateTimers(timerUpdate);
-    if (input != null) {
-      completedTransform.removePending(input);
-    }
 
+    // Newly pending elements must be added before completed elements are removed, as the two
+    // do not share a Mutex within this call and thus can be interleaved with external calls to
+    // refresh.
     for (CommittedBundle<?> bundle : outputs) {
       for (AppliedPTransform<?, ?, ?> consumer : consumers.get(bundle.getPCollection())) {
         TransformWatermarks watermarks = transformToWatermarks.get(consumer);
         watermarks.addPending(bundle);
       }
     }
+
+    completedTransform.updateTimers(timerUpdate);
+    if (input != null) {
+      completedTransform.removePending(input);
+    }
+
   }
 
   /**