diff --git a/flax/nnx/graphlib.py b/flax/nnx/graphlib.py
index a3a0aa8fb..8cef1d231 100644
--- a/flax/nnx/graphlib.py
+++ b/flax/nnx/graphlib.py
@@ -22,6 +22,7 @@
 import builtins
 
 import jax.core
+import jax.numpy as jnp
 
 from flax import config
 from flax.nnx import filterlib, reprlib, traversals, variablelib
@@ -2878,7 +2879,13 @@ def pop(
     return states
 
 
-def clone(node: Node, variables: bool = True, *, graph: bool | None = None) -> Node:
+def clone(
+  node: Node,
+  variables: bool = True,
+  *,
+  arrays: bool = False,
+  graph: bool | None = None,
+) -> Node:
   """Create a deep copy of the given graph node.
 
   Example usage::
@@ -2890,10 +2897,32 @@ def clone(node: Node, variables: bool = True, *, graph: bool | None = None) -> N
     >>> model.bias[...] += 1
     >>> assert (model.bias[...] != cloned_model.bias[...]).all()
 
+  When ``arrays=True``, the underlying JAX array buffers are also copied so
+  that the clone and the original share no physical memory.  This is needed
+  when the cloned model will be passed to a function with
+  ``donate_argnums``—without it both the original and the clone share the
+  same buffer, causing JAX to reject the donation with
+  *"the same buffer cannot be donated more than once"*.
+
+  Example with ``arrays=True``::
+
+    >>> import jax
+    >>> model = nnx.Linear(2, 3, rngs=nnx.Rngs(0))
+    >>> cloned_model = nnx.clone(model, arrays=True)
+    >>> # The buffers are now independent — safe to donate separately.
+    >>> model_ptr = model.bias[...].unsafe_buffer_pointer()
+    >>> clone_ptr = cloned_model.bias[...].unsafe_buffer_pointer()
+    >>> assert model_ptr != clone_ptr
+
   Args:
     node: A graph node object.
-    variables: If ``True`` (default) copies of the :class:`Variable` objects are created,
-      otherwise the Variables are shared between the original and cloned node.
+    variables: If ``True`` (default) copies of the :class:`Variable` objects
+      are created, otherwise the Variables are shared between the original and
+      cloned node.
+    arrays: If ``True``, replaces all shared JAX array buffers in the clone
+      with independent physical copies (using :func:`jax.numpy.array`).  This
+      has no effect when ``variables=False``.  Defaults to ``False`` to
+      preserve the existing copy-on-write behaviour.
     graph: If ``True`` (default), uses graph-mode which supports the full
       NNX feature set including shared references. If ``False``, uses
       tree-mode which treats Modules as regular JAX pytrees, avoiding
@@ -2902,7 +2931,20 @@ def clone(node: Node, variables: bool = True, *, graph: bool | None = None) -> N
     A deep copy of the :class:`Module` object.
   """
   graphdef, state = split(node, graph=graph)
-  return merge(graphdef, state, copy=variables)
+  merged = merge(graphdef, state, copy=variables)
+  if arrays and variables:
+    # Variable.copy() currently uses jax.tree.map(lambda x: x, value), which
+    # reconstructs the pytree wrapper but reuses the underlying JAX array
+    # buffer (copy-on-write semantics).  For donate_argnums compatibility we
+    # need each buffer to be physically independent.  We do a second pass over
+    # the cloned state and replace every jax.Array leaf with a fresh copy.
+    _, cloned_state = split(merged, graph=graph)
+    deep_state = jax.tree.map(
+      lambda x: jnp.array(x) if isinstance(x, jax.Array) else x,
+      cloned_state,
+    )
+    return merge(graphdef, deep_state, copy=False)
+  return merged
 
 
 def with_vars(
diff --git a/tests/nnx/module_test.py b/tests/nnx/module_test.py
index be350e8a9..fb79f7406 100644
--- a/tests/nnx/module_test.py
+++ b/tests/nnx/module_test.py
@@ -574,6 +574,43 @@ def test_clone(self):
     assert m.b.c.get_value() == m2.b.c.get_value()
     assert m.b.d.get_value() == m2.b.d.get_value()
 
+  def test_clone_arrays_true_creates_independent_buffers(self):
+    """Regression test for https://github.com/google/flax/issues/5461.
+
+    nnx.clone() with the default arrays=False uses copy-on-write semantics:
+    new Variable wrappers are created but the underlying jax.Array buffers
+    are shared.  This breaks donate_argnums because JAX sees the same buffer
+    donated twice.
+
+    With arrays=True, all array buffers are physically independent.
+    """
+    model = nnx.Linear(2, 3, rngs=nnx.Rngs(0))
+    cloned = nnx.clone(model, arrays=True)
+
+    # Values must be equal.
+    np.testing.assert_array_equal(
+        model.kernel[...], cloned.kernel[...])
+    np.testing.assert_array_equal(
+        model.bias[...], cloned.bias[...])
+
+    # Physical buffers must be distinct.
+    assert (model.kernel.get_value().unsafe_buffer_pointer() !=
+            cloned.kernel.get_value().unsafe_buffer_pointer()), (
+        'arrays=True should produce independent buffers, but kernel still '
+        'shares memory with the original')
+    assert (model.bias.get_value().unsafe_buffer_pointer() !=
+            cloned.bias.get_value().unsafe_buffer_pointer()), (
+        'arrays=True should produce independent buffers, but bias still '
+        'shares memory with the original')
+
+  def test_clone_arrays_false_default_preserves_copy_on_write(self):
+    """Default clone (arrays=False) still diverges on mutation."""
+    model = nnx.Linear(2, 3, rngs=nnx.Rngs(0))
+    cloned = nnx.clone(model)           # arrays=False is the default
+    model.bias[...] += 1
+    assert (model.bias[...] != cloned.bias[...]).all(), (
+        'Default clone should diverge after in-place mutation')
+
   def test_sow_existing_non_variable_field(self):
     class Foo(nnx.Module):
       def __init__(self) -> None: