diff --git a/src/spatialdata/_core/spatialdata.py b/src/spatialdata/_core/spatialdata.py
index 1b6a17127..98fd391c6 100644
--- a/src/spatialdata/_core/spatialdata.py
+++ b/src/spatialdata/_core/spatialdata.py
@@ -108,8 +108,10 @@ class SpatialData:
         - images and labels are stored as :class:`xarray.DataArray` or :class:`xarray.DataTree` objects.
         - points are stored as :class:`dask.dataframe.DataFrame` objects.
         - shapes are stored as :class:`geopandas.GeoDataFrame`.
-        - the table are stored as :class:`anndata.AnnData` objects,  with the spatial coordinates stored in the obsm
-            slot.
+        - tables are stored as :class:`anndata.AnnData` objects. Tables have no coordinate system: coordinates
+          stored in a table (e.g. in ``obsm["spatial"]``, the squidpy/scanpy convention that several spatialdata-io
+          readers populate) are currently not transformed or used by spatial queries, and can get out of sync with
+          the SpatialElements the table annotates.
 
     Tables can annotate SpatialElements (labels, shapes or points) and can be used to store additional
     information. Points can also store annotations directly, as additional dataframe columns.