diff --git a/src/hdmf_zarr/backend.py b/src/hdmf_zarr/backend.py
index 1636487c..51109946 100644
--- a/src/hdmf_zarr/backend.py
+++ b/src/hdmf_zarr/backend.py
@@ -755,7 +755,10 @@ def resolve_ref(self, zarr_ref):
             source_file = str(zarr_ref['source'])
         # Resolve the path relative to the current file
         if not self.is_remote():
-            source_file = os.path.abspath(os.path.join(self.source, source_file))
+            if isinstance(self.source, str) and self.source.startswith(("s3://")):
+                source_file = self.source
+            else:
+                source_file = os.path.abspath(os.path.join(self.source, source_file))
         else:
             # get rid of extra "/" and "./" in the path root and source_file
             root_path = str(self.path).rstrip("/")