diff --git a/pkgs/development/python-modules/multiscale-spatial-image/default.nix b/pkgs/development/python-modules/multiscale-spatial-image/default.nix
index 41b4a720fc50..939e144c2c0e 100644
--- a/pkgs/development/python-modules/multiscale-spatial-image/default.nix
+++ b/pkgs/development/python-modules/multiscale-spatial-image/default.nix
@@ -9,7 +9,6 @@
   python-dateutil,
   spatial-image,
   xarray,
-  xarray-datatree,
   zarr,
   dask-image,
   fsspec,
@@ -23,7 +22,7 @@
 
 buildPythonPackage rec {
   pname = "multiscale-spatial-image";
-  version = "1.0.1";
+  version = "2.0.0";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -32,7 +31,7 @@ buildPythonPackage rec {
     owner = "spatial-image";
     repo = "multiscale-spatial-image";
     rev = "refs/tags/v${version}";
-    hash = "sha256-s/88N8IVkj+9MZYAtEJSpmmDdjIxf4S6U5gYr86Ikrw=";
+    hash = "sha256-SNAbkFgShb1FSM4tXoyf2L27LmpWznMThgAVfJwI00A=";
   };
 
   build-system = [ hatchling ];
@@ -43,7 +42,6 @@ buildPythonPackage rec {
     python-dateutil
     spatial-image
     xarray
-    xarray-datatree
     zarr
   ];
 
diff --git a/pkgs/development/python-modules/xarray-datatree/default.nix b/pkgs/development/python-modules/xarray-datatree/default.nix
deleted file mode 100644
index 1d99f300cb7b..000000000000
--- a/pkgs/development/python-modules/xarray-datatree/default.nix
+++ /dev/null
@@ -1,59 +0,0 @@
-{
-  lib,
-  buildPythonPackage,
-  fetchFromGitHub,
-  pythonOlder,
-  check-manifest,
-  setuptools,
-  setuptools-scm,
-  packaging,
-  pytestCheckHook,
-  xarray,
-  zarr,
-}:
-
-buildPythonPackage rec {
-  pname = "datatree";
-  version = "0.0.14";
-  pyproject = true;
-
-  disabled = pythonOlder "3.9";
-
-  src = fetchFromGitHub {
-    owner = "xarray-contrib";
-    repo = "datatree";
-    rev = "refs/tags/v${version}";
-    hash = "sha256-C6+WcHc2+sftJ5Yyh/9TTIHhAEwhAqSsSkaDwtq7J90=";
-  };
-
-  build-system = [
-    check-manifest
-    setuptools
-    setuptools-scm
-  ];
-
-  dependencies = [
-    packaging
-    xarray
-  ];
-
-  nativeCheckInputs = [
-    pytestCheckHook
-    zarr
-  ];
-
-  pythonImportsCheck = [ "datatree" ];
-
-  disabledTests = [
-    # output formatting issue, likely due to underlying library version difference:
-    "test_diff_node_data"
-  ];
-
-  meta = with lib; {
-    description = "Tree-like hierarchical data structure for xarray";
-    homepage = "https://xarray-datatree.readthedocs.io";
-    changelog = "https://github.com/xarray-contrib/datatree/releases/tag/v${version}";
-    license = licenses.asl20;
-    maintainers = with maintainers; [ bcdarwin ];
-  };
-}
diff --git a/pkgs/development/python-modules/xarray/default.nix b/pkgs/development/python-modules/xarray/default.nix
index 2696b2574326..96540a3484b6 100644
--- a/pkgs/development/python-modules/xarray/default.nix
+++ b/pkgs/development/python-modules/xarray/default.nix
@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "xarray";
-  version = "2024.09.0";
+  version = "2024.10.0";
   pyproject = true;
 
   disabled = pythonOlder "3.10";
@@ -22,7 +22,7 @@ buildPythonPackage rec {
     owner = "pydata";
     repo = "xarray";
     rev = "refs/tags/v${version}";
-    hash = "sha256-ZrqdpzcNjZMxET355PRWQaUPjvFm+m2y71F7qt8DCjg=";
+    hash = "sha256-s5MvHp2OkomD3xNYzj9oKlVLMgHZDQRBJM6vgOAv1jQ=";
   };
 
   build-system = [
diff --git a/pkgs/top-level/python-aliases.nix b/pkgs/top-level/python-aliases.nix
index fbe15f318a1b..1d623b069c36 100644
--- a/pkgs/top-level/python-aliases.nix
+++ b/pkgs/top-level/python-aliases.nix
@@ -702,6 +702,7 @@ mapAliases ({
   WSME = wsme; # added 2023-02-19
   x11_hash = x11-hash; # added 2023-11-05
   xapp = python-xapp; # added 2024-07-19
+  xarray-datatree = throw "Datatree has been merged upstream into pydata/xarray, and released as of xarray version 2024.10.0."; # added 2024-11-02
   xenomapper = throw "xenomapper was moved to pkgs.xenomapper"; # added 2021-12-31
   XlsxWriter = xlsxwriter; # added 2023-02-19
   xsser = "xsser has been removed because it was unmaintained and relies on a archived project"; # added 2024-07-27
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 6f9e572d92a3..1cc47777528b 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -17771,8 +17771,6 @@ self: super: with self; {
 
   xarray-dataclasses = callPackage ../development/python-modules/xarray-dataclasses { };
 
-  xarray-datatree = callPackage ../development/python-modules/xarray-datatree { };
-
   xarray-einstats = callPackage ../development/python-modules/xarray-einstats { };
 
   xattr = callPackage ../development/python-modules/xattr { };