diff --git a/.changeset/dull-pumas-punch.md b/.changeset/dull-pumas-punch.md
new file mode 100644
index 000000000..fb69ff215
--- /dev/null
+++ b/.changeset/dull-pumas-punch.md
@@ -0,0 +1,9 @@
+---
+'@powersync/service-module-mongodb-storage': patch
+'@powersync/service-errors': patch
+'@powersync/lib-service-mongodb': patch
+'@powersync/service-core': patch
+'@powersync/service-image': patch
+---
+
+[MongoDB Storage] Improve error messages for checksum query timeouts
diff --git a/libs/lib-mongodb/src/db/errors.ts b/libs/lib-mongodb/src/db/errors.ts
index 2c5eb183f..85b0838ee 100644
--- a/libs/lib-mongodb/src/db/errors.ts
+++ b/libs/lib-mongodb/src/db/errors.ts
@@ -1,4 +1,9 @@
-import { DatabaseConnectionError, ErrorCode, ServiceError } from '@powersync/lib-services-framework';
+import {
+  DatabaseConnectionError,
+  DatabaseQueryError,
+  ErrorCode,
+  ServiceError
+} from '@powersync/lib-services-framework';
 import { isMongoServerError } from './mongo.js';
 import { MongoNetworkError, MongoServerSelectionError } from 'mongodb';
 
@@ -58,6 +63,22 @@ export function mapConnectionError(err: any): ServiceError {
   }
 }
 
+export function mapQueryError(err: any, context: string): ServiceError {
+  if (ServiceError.isServiceError(err)) {
+    return err;
+  } else if (isMongoServerError(err)) {
+    if (err.codeName == 'MaxTimeMSExpired') {
+      return new DatabaseQueryError(ErrorCode.PSYNC_S2403, `Query timed out ${context}`, err);
+    }
+
+    // Fallback
+    return new DatabaseQueryError(ErrorCode.PSYNC_S2404, `MongoDB server error ${context}: ${err.codeName}`, err);
+  } else {
+    // Fallback
+    return new DatabaseQueryError(ErrorCode.PSYNC_S2404, `MongoDB connection error ${context}`, err);
+  }
+}
+
 function isNetworkError(err: any): err is MongoNetworkError {
   return err?.name === 'MongoNetworkError';
 }
diff --git a/libs/lib-mongodb/src/db/mongo.ts b/libs/lib-mongodb/src/db/mongo.ts
index 059c4facd..b8f8ff170 100644
--- a/libs/lib-mongodb/src/db/mongo.ts
+++ b/libs/lib-mongodb/src/db/mongo.ts
@@ -19,7 +19,7 @@ export const MONGO_SOCKET_TIMEOUT_MS = 60_000;
  *
  * Must be less than MONGO_SOCKET_TIMEOUT_MS to ensure proper error handling.
  */
-export const MONGO_OPERATION_TIMEOUT_MS = 30_000;
+export const MONGO_OPERATION_TIMEOUT_MS = 40_000;
 
 /**
  * Same as above, but specifically for clear operations.
diff --git a/modules/module-mongodb-storage/src/storage/implementation/MongoSyncBucketStorage.ts b/modules/module-mongodb-storage/src/storage/implementation/MongoSyncBucketStorage.ts
index 676ef7130..d069d28f6 100644
--- a/modules/module-mongodb-storage/src/storage/implementation/MongoSyncBucketStorage.ts
+++ b/modules/module-mongodb-storage/src/storage/implementation/MongoSyncBucketStorage.ts
@@ -348,7 +348,10 @@ export class MongoSyncBucketStorage
         // 1. We can calculate the document size accurately without serializing again.
         // 2. We can delay parsing the results until it's needed.
         // We manually use bson.deserialize below
-        raw: true
+        raw: true,
+
+        // Limit the time for the operation to complete, to avoid getting connection timeouts
+        maxTimeMS: lib_mongo.db.MONGO_OPERATION_TIMEOUT_MS
       }
     ) as unknown as mongo.FindCursor<Buffer>;
 
@@ -357,7 +360,9 @@ export class MongoSyncBucketStorage
     // to the lower of the batch count and size limits.
     // This is similar to using `singleBatch: true` in the find options, but allows
     // detecting "hasMore".
-    let { data, hasMore: batchHasMore } = await readSingleBatch(cursor);
+    let { data, hasMore: batchHasMore } = await readSingleBatch(cursor).catch((e) => {
+      throw lib_mongo.mapQueryError(e, 'while reading bucket data');
+    });
     if (data.length == batchLimit) {
       // Limit reached - could have more data, despite the cursor being drained.
       batchHasMore = true;
@@ -486,9 +491,12 @@ export class MongoSyncBucketStorage
             }
           }
         ],
-        { session: undefined, readConcern: 'snapshot' }
+        { session: undefined, readConcern: 'snapshot', maxTimeMS: lib_mongo.db.MONGO_OPERATION_TIMEOUT_MS }
       )
-      .toArray();
+      .toArray()
+      .catch((e) => {
+        throw lib_mongo.mapQueryError(e, 'while reading checksums');
+      });
 
     return new Map<string, storage.PartialChecksum>(
       aggregate.map((doc) => {
diff --git a/packages/service-errors/src/codes.ts b/packages/service-errors/src/codes.ts
index 64e70c619..74f92a73f 100644
--- a/packages/service-errors/src/codes.ts
+++ b/packages/service-errors/src/codes.ts
@@ -428,6 +428,17 @@ export enum ErrorCode {
    */
   PSYNC_S2402 = 'PSYNC_S2402',
 
+  /**
+   * Query timed out. Could be due to a large query or a temporary load issue on the storage database.
+   * Retry the request.
+   */
+  PSYNC_S2403 = 'PSYNC_S2403',
+
+  /**
+   * Query failure on the storage database. See error details for more information.
+   */
+  PSYNC_S2404 = 'PSYNC_S2404',
+
   // ## PSYNC_S23xx: Sync API errors - Postgres Storage
 
   // ## PSYNC_S3xxx: Service configuration issues
diff --git a/packages/service-errors/src/errors.ts b/packages/service-errors/src/errors.ts
index a9a6fe593..fdafcfca9 100644
--- a/packages/service-errors/src/errors.ts
+++ b/packages/service-errors/src/errors.ts
@@ -243,3 +243,19 @@ export class DatabaseConnectionError extends ServiceError {
     this.cause = cause;
   }
 }
+
+export class DatabaseQueryError extends ServiceError {
+  public cause: any;
+
+  constructor(code: ErrorCode, message: string, cause?: any) {
+    super({
+      code: code,
+      status: 500,
+      description: message,
+      // Cause is always logged. Return details via the API only in development mode
+      details: process.env.NODE_ENV !== 'production' && cause != null ? `cause: ${cause.message}` : undefined,
+      stack: process.env.NODE_ENV !== 'production' ? cause.stack : undefined
+    });
+    this.cause = cause;
+  }
+}