diff --git a/pkgs/development/python-modules/numpy/2.nix b/pkgs/development/python-modules/numpy/2.nix
index e0856c05ca5c..e3f8a01cdb3d 100644
--- a/pkgs/development/python-modules/numpy/2.nix
+++ b/pkgs/development/python-modules/numpy/2.nix
@@ -59,7 +59,7 @@ let
 in
 buildPythonPackage rec {
   pname = "numpy";
-  version = "2.3.0";
+  version = "2.3.1";
   pyproject = true;
 
   disabled = pythonOlder "3.10";
@@ -67,7 +67,7 @@ buildPythonPackage rec {
   src = fetchPypi {
     inherit pname version;
     extension = "tar.gz";
-    hash = "sha256-WB+H+enp2yy6IUFADhYOndZE7iSHiNb5BjbuuP2SYKY=";
+    hash = "sha256-HsmuIKQibaN0NizKPGLNdT+vL5UUQLDjuY6TwjVEHSs=";
   };
 
   patches = lib.optionals python.hasDistutilsCxxPatch [
diff --git a/pkgs/development/python-modules/pythran/default.nix b/pkgs/development/python-modules/pythran/default.nix
index bd88addc6148..a20b4ecf5373 100644
--- a/pkgs/development/python-modules/pythran/default.nix
+++ b/pkgs/development/python-modules/pythran/default.nix
@@ -24,14 +24,14 @@ let
 in
 buildPythonPackage rec {
   pname = "pythran";
-  version = "0.17.0";
+  version = "0.18.0";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "serge-sans-paille";
     repo = "pythran";
     tag = version;
-    hash = "sha256-JG1FH2UAekFF9Vv7wCn/L7gJlVKv5AxqgGrj8pejqeY=";
+    hash = "sha256-GZSVcB4JIx02eiUb9d7o5cUAyICIoH6m0mz4TL7a9PY=";
   };
 
   patches = [
diff --git a/pkgs/development/python-modules/scipy/default.nix b/pkgs/development/python-modules/scipy/default.nix
index f6eccfe6da32..f08228330bc7 100644
--- a/pkgs/development/python-modules/scipy/default.nix
+++ b/pkgs/development/python-modules/scipy/default.nix
@@ -48,8 +48,8 @@ let
   #     nix-shell maintainers/scripts/update.nix --argstr package python3.pkgs.scipy
   #
   # The update script uses sed regexes to replace them with the updated hashes.
-  version = "1.15.3";
-  srcHash = "sha256-97z5CLRq/2kWjL2+ewHRA71vSfvCLHVJdOUZfDFnyhM=";
+  version = "1.16.0";
+  srcHash = "sha256-PFWUq7RsqMgBK1bTw52y1renoPygWNreikNTFHWE2Ig=";
   datasetsHashes = {
     ascent = "1qjp35ncrniq9rhzb14icwwykqg2208hcssznn3hz27w39615kh3";
     ecg = "1bwbjp43b7znnwha5hv6wiz3g0bhwrpqpi75s12zidxrbwvd62pj";
@@ -104,7 +104,7 @@ buildPythonPackage {
   # that override globally the `numpy` attribute to point to `numpy_1`.
   postPatch = ''
     substituteInPlace pyproject.toml \
-      --replace-fail "numpy>=2.0.0,<2.5" numpy
+      --replace-fail "numpy>=2.0.0,<2.6" numpy
   '';
 
   build-system =
@@ -119,7 +119,7 @@ buildPythonPackage {
     ]
     ++ lib.optionals stdenv.hostPlatform.isDarwin [
       # Minimal version required according to:
-      # https://github.com/scipy/scipy/blob/v1.14.0/scipy/meson.build#L185-L188
+      # https://github.com/scipy/scipy/blob/v1.16.0/scipy/meson.build#L238-L244
       (xcbuild.override {
         sdkVer = "13.3";
       })
@@ -143,23 +143,17 @@ buildPythonPackage {
     pytest-xdist
   ];
 
-  disabledTests =
-    [
-      "test_cumulative_simpson_against_simpson_with_default_dx"
-      # https://github.com/scipy/scipy/issues/22789
-      "test_funcs"
-    ]
-    ++ lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64) [
-      # The following tests are broken on aarch64-darwin with newer compilers and library versions.
-      # See https://github.com/scipy/scipy/issues/18308
-      "test_a_b_neg_int_after_euler_hypergeometric_transformation"
-      "test_dst4_definition_ortho"
-      "test_load_mat4_le"
-      "hyp2f1_test_case47"
-      "hyp2f1_test_case3"
-      "test_uint64_max"
-      "test_large_m4" # https://github.com/scipy/scipy/issues/22466
-    ];
+  disabledTests = lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64) [
+    # The following tests are broken on aarch64-darwin with newer compilers and library versions.
+    # See https://github.com/scipy/scipy/issues/18308
+    "test_a_b_neg_int_after_euler_hypergeometric_transformation"
+    "test_dst4_definition_ortho"
+    "test_load_mat4_le"
+    "hyp2f1_test_case47"
+    "hyp2f1_test_case3"
+    "test_uint64_max"
+    "test_large_m4" # https://github.com/scipy/scipy/issues/22466
+  ];
 
   doCheck = !(stdenv.hostPlatform.isx86_64 && stdenv.hostPlatform.isDarwin);