diff --git a/pkgs/by-name/gd/gdal/package.nix b/pkgs/by-name/gd/gdal/package.nix
index 643f2c5c08f2..e788c5123485 100644
--- a/pkgs/by-name/gd/gdal/package.nix
+++ b/pkgs/by-name/gd/gdal/package.nix
@@ -68,7 +68,7 @@
   pkg-config,
   poppler,
   proj,
-  python3,
+  python3Packages,
   qhull,
   rav1e,
   sqlite,
@@ -98,8 +98,8 @@ stdenv.mkDerivation (finalAttrs: {
     doxygen
     graphviz
     pkg-config
-    python3.pkgs.setuptools
-    python3.pkgs.wrapPython
+    python3Packages.setuptools
+    python3Packages.wrapPython
     swig
   ]
   ++ lib.optionals useJava [
@@ -202,8 +202,8 @@ stdenv.mkDerivation (finalAttrs: {
       libwebp
       zlib
       zstd
-      python3
-      python3.pkgs.numpy
+      python3Packages.python
+      python3Packages.numpy
     ]
     ++ tileDbDeps
     ++ libAvifDeps
@@ -219,7 +219,7 @@ stdenv.mkDerivation (finalAttrs: {
     ++ darwinDeps
     ++ nonDarwinDeps;
 
-  pythonPath = [ python3.pkgs.numpy ];
+  pythonPath = [ python3Packages.numpy ];
   postInstall = ''
     wrapPythonProgramsIn "$out/bin" "$out $pythonPath"
   ''
@@ -238,14 +238,14 @@ stdenv.mkDerivation (finalAttrs: {
     pushd autotest
 
     export HOME=$(mktemp -d)
-    export PYTHONPATH="$out/${python3.sitePackages}:$PYTHONPATH"
+    export PYTHONPATH="$out/${python3Packages.python.sitePackages}:$PYTHONPATH"
     export GDAL_DOWNLOAD_TEST_DATA=OFF
     # allows to skip tests that fail because of file handle leak
     # the issue was not investigated
     # https://github.com/OSGeo/gdal/blob/v3.9.0/autotest/gdrivers/bag.py#L54
     export CI=1
   '';
-  nativeInstallCheckInputs = with python3.pkgs; [
+  nativeInstallCheckInputs = with python3Packages; [
     pytestCheckHook
     pytest-benchmark
     pytest-env
diff --git a/pkgs/development/libraries/vtk/generic.nix b/pkgs/development/libraries/vtk/generic.nix
index 587984f4768b..3593e438f794 100644
--- a/pkgs/development/libraries/vtk/generic.nix
+++ b/pkgs/development/libraries/vtk/generic.nix
@@ -111,6 +111,8 @@ let
     adios2 = self.callPackage adios2.override { };
     cgns = self.callPackage cgns.override { };
     viskores = self.callPackage viskores.override { };
+    gdal = self.callPackage gdal.override { useMinimalFeatures = true; };
+    pdal = self.callPackage pdal.override { };
   });
   vtkBool = feature: bool: lib.cmakeFeature feature "${if bool then "YES" else "NO"}";
 in
@@ -137,8 +139,6 @@ stdenv.mkDerivation (finalAttrs: {
 
   buildInputs = [
     libLAS
-    gdal
-    pdal
     alembic
     imath
     c-blosc
@@ -152,6 +152,8 @@ stdenv.mkDerivation (finalAttrs: {
     libarchive
     libGL
     openvdb
+    vtkPackages.gdal
+    vtkPackages.pdal
   ]
   ++ lib.optionals stdenv.hostPlatform.isLinux [
     libXfixes
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 44efe9f0b40f..aea8bd4d2f54 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -5948,7 +5948,7 @@ self: super: with self; {
 
   gcsfs = callPackage ../development/python-modules/gcsfs { };
 
-  gdal = toPythonModule (pkgs.gdal.override { python3 = python; });
+  gdal = toPythonModule (pkgs.gdal.override { python3Packages = self; });
 
   gdata = callPackage ../development/python-modules/gdata { };