diff --git a/asv_bench/benchmarks/indexing.py b/asv_bench/benchmarks/indexing.py
index cd212895d99..c4cfbbbdfdf 100644
--- a/asv_bench/benchmarks/indexing.py
+++ b/asv_bench/benchmarks/indexing.py
@@ -125,3 +125,16 @@ def setup(self, key):
         requires_dask()
         super().setup(key)
         self.ds = self.ds.chunk({"x": 100, "y": 50, "t": 50})
+
+
+class BooleanIndexing:
+    # https://github.com/pydata/xarray/issues/2227
+    def setup(self):
+        self.ds = xr.Dataset(
+            {"a": ("time", np.arange(10_000_000))},
+            coords={"time": np.arange(10_000_000)},
+        )
+        self.time_filter = self.ds.time > 50_000
+
+    def time_indexing(self):
+        self.ds.isel(time=self.time_filter)
diff --git a/doc/whats-new.rst b/doc/whats-new.rst
index 1268f7f3982..e460e1e230c 100644
--- a/doc/whats-new.rst
+++ b/doc/whats-new.rst
@@ -24,6 +24,13 @@ New functions/methods
 
 - Added :py:func:`~xarray.map_blocks`, modeled after :py:func:`dask.array.map_blocks`
   By `Deepak Cherian <https://github.com/dcherian>`_.
+Bug fixes
+~~~~~~~~~
+- Reintroduce support for :mod:`weakref` (broken in v0.13.0). Support has been
+  reinstated for :class:`DataArray` and :class:`Dataset` objects only. Internal xarray
+  objects remain unaddressable by weakref in order to save memory.
+  (:issue:`3317`) by `Guido Imperiale <https://github.com/crusaderky>`_.
+
 
 .. _whats-new.0.13.0:
 
@@ -32,7 +39,7 @@ v0.13.0 (17 Sep 2019)
 
 This release includes many exciting changes: wrapping of
 `NEP18 <https://www.numpy.org/neps/nep-0018-array-function-protocol.html>`_ compliant
-numpy-like arrays; new :py:meth:`~Dataset.plot.scatter` method that can scatter
+numpy-like arrays; new :py:meth:`~Dataset.plot.scatter` plotting method that can scatter
 two ``DataArrays`` in a ``Dataset`` against each other; support for converting pandas
 DataFrames to xarray objects that wrap ``pydata/sparse``; and more!
 
diff --git a/xarray/core/dataarray.py b/xarray/core/dataarray.py
index 21643694d5b..690b73d12b3 100644
--- a/xarray/core/dataarray.py
+++ b/xarray/core/dataarray.py
@@ -248,7 +248,15 @@ class DataArray(AbstractArray, DataWithCoords):
         Dictionary for holding arbitrary metadata.
     """
 
-    __slots__ = ("_accessors", "_coords", "_file_obj", "_name", "_indexes", "_variable")
+    __slots__ = (
+        "_accessors",
+        "_coords",
+        "_file_obj",
+        "_name",
+        "_indexes",
+        "_variable",
+        "__weakref__",
+    )
 
     _groupby_cls = groupby.DataArrayGroupBy
     _rolling_cls = rolling.DataArrayRolling
diff --git a/xarray/core/dataset.py b/xarray/core/dataset.py
index eaffb5b7387..25ea2a873e9 100644
--- a/xarray/core/dataset.py
+++ b/xarray/core/dataset.py
@@ -420,6 +420,7 @@ class Dataset(Mapping, ImplementsDatasetReduce, DataWithCoords):
         "_file_obj",
         "_indexes",
         "_variables",
+        "__weakref__",
     )
 
     _groupby_cls = groupby.DatasetGroupBy
@@ -1783,7 +1784,7 @@ def _validate_indexers(
             elif isinstance(v, Dataset):
                 raise TypeError("cannot use a Dataset as an indexer")
             elif isinstance(v, Sequence) and len(v) == 0:
-                v = IndexVariable((k,), np.zeros((0,), dtype="int64"))
+                v = Variable((k,), np.zeros((0,), dtype="int64"))
             else:
                 v = np.asarray(v)
 
@@ -1797,16 +1798,13 @@ def _validate_indexers(
                 if v.ndim == 0:
                     v = Variable((), v)
                 elif v.ndim == 1:
-                    v = IndexVariable((k,), v)
+                    v = Variable((k,), v)
                 else:
                     raise IndexError(
                         "Unlabeled multi-dimensional array cannot be "
                         "used for indexing: {}".format(k)
                     )
 
-            if v.ndim == 1:
-                v = v.to_index_variable()
-
             indexers_list.append((k, v))
 
         return indexers_list
@@ -2369,7 +2367,10 @@ def interp(
         if kwargs is None:
             kwargs = {}
         coords = either_dict_or_kwargs(coords, coords_kwargs, "interp")
-        indexers = OrderedDict(self._validate_indexers(coords))
+        indexers = OrderedDict(
+            (k, v.to_index_variable() if isinstance(v, Variable) and v.ndim == 1 else v)
+            for k, v in self._validate_indexers(coords)
+        )
 
         obj = self if assume_sorted else self.sortby([k for k in coords])
 
diff --git a/xarray/tests/test_dataarray.py b/xarray/tests/test_dataarray.py
index 01e92bdd7be..9ba3eecc5a0 100644
--- a/xarray/tests/test_dataarray.py
+++ b/xarray/tests/test_dataarray.py
@@ -4672,3 +4672,14 @@ class MyArray(DataArray):
             pass
 
     assert str(e.value) == "MyArray must explicitly define __slots__"
+
+
+def test_weakref():
+    """Classes with __slots__ are incompatible with the weakref module unless they
+    explicitly state __weakref__ among their slots
+    """
+    from weakref import ref
+
+    a = DataArray(1)
+    r = ref(a)
+    assert r() is a
diff --git a/xarray/tests/test_dataset.py b/xarray/tests/test_dataset.py
index 7d2b11d02c9..f02990a1be9 100644
--- a/xarray/tests/test_dataset.py
+++ b/xarray/tests/test_dataset.py
@@ -5786,3 +5786,14 @@ class MyDS(Dataset):
             pass
 
     assert str(e.value) == "MyDS must explicitly define __slots__"
+
+
+def test_weakref():
+    """Classes with __slots__ are incompatible with the weakref module unless they
+    explicitly state __weakref__ among their slots
+    """
+    from weakref import ref
+
+    ds = Dataset()
+    r = ref(ds)
+    assert r() is ds