diff --git a/docs/releases.rst b/docs/releases.rst
index 53d99207..6a9ae28c 100644
--- a/docs/releases.rst
+++ b/docs/releases.rst
@@ -39,10 +39,11 @@ Bug fixes
 Documentation
 ~~~~~~~~~~~~~
 
+- Warn if user passes `indexes=None` to `open_virtual_dataset` to indicate that this is not yet fully supported.
+  (:pull:`170`) By `Tom Nicholas <https://github.com/TomNicholas>`_.
 - Clarify that virtual datasets cannot be treated like normal xarray datasets. (:issue:`173`)
   By `Tom Nicholas <https://github.com/TomNicholas>`_.
 
-
 Internal Changes
 ~~~~~~~~~~~~~~~~
 
diff --git a/virtualizarr/tests/test_integration.py b/virtualizarr/tests/test_integration.py
index 256ed363..2e612de9 100644
--- a/virtualizarr/tests/test_integration.py
+++ b/virtualizarr/tests/test_integration.py
@@ -173,5 +173,5 @@ def test_open_scalar_variable(tmpdir):
     ds = xr.Dataset(data_vars={"a": 0})
     ds.to_netcdf(f"{tmpdir}/scalar.nc")
 
-    vds = open_virtual_dataset(f"{tmpdir}/scalar.nc")
+    vds = open_virtual_dataset(f"{tmpdir}/scalar.nc", indexes={})
     assert vds["a"].shape == ()
diff --git a/virtualizarr/tests/test_xarray.py b/virtualizarr/tests/test_xarray.py
index b1665a07..d0fe2e3b 100644
--- a/virtualizarr/tests/test_xarray.py
+++ b/virtualizarr/tests/test_xarray.py
@@ -251,7 +251,8 @@ def test_no_indexes(self, netcdf4_file):
         assert vds.indexes == {}
 
     def test_create_default_indexes(self, netcdf4_file):
-        vds = open_virtual_dataset(netcdf4_file, indexes=None)
+        with pytest.warns(UserWarning, match="will create in-memory pandas indexes"):
+            vds = open_virtual_dataset(netcdf4_file, indexes=None)
         ds = xr.open_dataset(netcdf4_file, decode_times=False)
 
         # TODO use xr.testing.assert_identical(vds.indexes, ds.indexes) instead once class supported by assertion comparison, see https://github.com/pydata/xarray/issues/5812
@@ -278,8 +279,10 @@ class TestCombineUsingIndexes:
     def test_combine_by_coords(self, netcdf4_files):
         filepath1, filepath2 = netcdf4_files
 
-        vds1 = open_virtual_dataset(filepath1)
-        vds2 = open_virtual_dataset(filepath2)
+        with pytest.warns(UserWarning, match="will create in-memory pandas indexes"):
+            vds1 = open_virtual_dataset(filepath1)
+        with pytest.warns(UserWarning, match="will create in-memory pandas indexes"):
+            vds2 = open_virtual_dataset(filepath2)
 
         combined_vds = xr.combine_by_coords(
             [vds2, vds1],
@@ -287,6 +290,23 @@ def test_combine_by_coords(self, netcdf4_files):
 
         assert combined_vds.xindexes["time"].to_pandas_index().is_monotonic_increasing
 
+    @pytest.mark.xfail(reason="Not yet implemented, see issue #18")
+    def test_combine_by_coords_keeping_manifestarrays(self, netcdf4_files):
+        filepath1, filepath2 = netcdf4_files
+
+        with pytest.warns(UserWarning, match="will create in-memory pandas indexes"):
+            vds1 = open_virtual_dataset(filepath1)
+        with pytest.warns(UserWarning, match="will create in-memory pandas indexes"):
+            vds2 = open_virtual_dataset(filepath2)
+
+        combined_vds = xr.combine_by_coords(
+            [vds2, vds1],
+        )
+
+        assert isinstance(combined_vds["time"].data, ManifestArray)
+        assert isinstance(combined_vds["lat"].data, ManifestArray)
+        assert isinstance(combined_vds["lon"].data, ManifestArray)
+
 
 @network
 @requires_s3fs
@@ -363,7 +383,9 @@ def test_read_from_url(self, filetype, url):
 class TestLoadVirtualDataset:
     def test_loadable_variables(self, netcdf4_file):
         vars_to_load = ["air", "time"]
-        vds = open_virtual_dataset(netcdf4_file, loadable_variables=vars_to_load)
+        vds = open_virtual_dataset(
+            netcdf4_file, loadable_variables=vars_to_load, indexes={}
+        )
 
         for name in vds.variables:
             if name in vars_to_load:
diff --git a/virtualizarr/xarray.py b/virtualizarr/xarray.py
index f33fc13f..df847173 100644
--- a/virtualizarr/xarray.py
+++ b/virtualizarr/xarray.py
@@ -1,3 +1,4 @@
+import warnings
 from collections.abc import Iterable, Mapping, MutableMapping
 from pathlib import Path
 from typing import (
@@ -156,6 +157,11 @@ def open_virtual_dataset(
             )
 
             if indexes is None:
+                warnings.warn(
+                    "Specifying `indexes=None` will create in-memory pandas indexes for each 1D coordinate, but concatenation of ManifestArrays backed by pandas indexes is not yet supported (see issue #18)."
+                    "You almost certainly want to pass `indexes={}` to `open_virtual_dataset` instead."
+                )
+
                 # add default indexes by reading data from file
                 indexes = {name: index for name, index in ds.xindexes.items()}
             elif indexes != {}: