diff --git a/pyproject.toml b/pyproject.toml
index 7426ff05518..a2ee09f849e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -365,21 +365,11 @@ filterwarnings = [
   "default::UserWarning:xarray.tests.test_coding_times",
   "default::UserWarning:xarray.tests.test_computation",
   "default::UserWarning:xarray.tests.test_dataset",
-  "default:`ancestors` has been deprecated:DeprecationWarning:xarray.core.treenode",
-  "default:`iter_lineage` has been deprecated:DeprecationWarning:xarray.core.treenode",
-  "default:`lineage` has been deprecated:DeprecationWarning:xarray.core.treenode",
-  "default:coords should be an ndarray:DeprecationWarning:xarray.tests.test_variable",
-  "default:deallocating CachingFileManager:RuntimeWarning:xarray.backends.*",
-  "default:deallocating CachingFileManager:RuntimeWarning:xarray.backends.netCDF4_",
-  "default:deallocating CachingFileManager:RuntimeWarning:xarray.core.indexing",
   "default:Failed to decode variable.*NumPy will stop allowing conversion of out-of-bound Python integers to integer arrays:DeprecationWarning",
   "default:The `interpolation` argument to quantile was renamed to `method`:FutureWarning:xarray.*",
-  "default:invalid value encountered in cast:RuntimeWarning:xarray.core.duck_array_ops",
   "default:invalid value encountered in cast:RuntimeWarning:xarray.conventions",
   "default:invalid value encountered in cast:RuntimeWarning:xarray.tests.test_units",
-  "default:invalid value encountered in cast:RuntimeWarning:xarray.tests.test_array_api",
   "default:NumPy will stop allowing conversion of:DeprecationWarning",
-  "default:shape should be provided:DeprecationWarning:xarray.tests.test_variable",
   "default:the `pandas.MultiIndex` object:FutureWarning:xarray.tests.test_variable",
   "default:Using a non-tuple sequence for multidimensional indexing is deprecated:FutureWarning",
   "default:Duplicate dimension names present:UserWarning:xarray.namedarray.core",