diff --git a/pkgs/development/libraries/gdal/default.nix b/pkgs/development/libraries/gdal/default.nix
index e7a999488827..f8bf3f7c075a 100644
--- a/pkgs/development/libraries/gdal/default.nix
+++ b/pkgs/development/libraries/gdal/default.nix
@@ -80,20 +80,20 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "gdal" + lib.optionalString useMinimalFeatures "-minimal";
-  version = "3.8.5";
+  version = "3.9.0";
 
   src = fetchFromGitHub {
     owner = "OSGeo";
     repo = "gdal";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-Z+mYlyOX9vJ772qwZMQfCbD/V7RL6+9JLHTzoZ55ot0=";
+    hash = "sha256-xEekgF9GzsPYkwk7Nny9b1DMLTxBqTSdudYxaz4jl/c=";
   };
 
   patches = [
-    # bump java source option to fix build with JDK 21
+    # HDF5: add support for libhdf5 >= 1.14.4.2 when built with Float16
     (fetchpatch {
-      url = "https://github.com/OSGeo/gdal/commit/ca2eb4130750b0e6365f738a5f8ff77081f5c5bb.patch";
-      sha256 = "sha256-wShYm9yA7twJR72co+Tvf/IuYXqbI0OrjWl0uqC3bwo=";
+      url = "https://github.com/OSGeo/gdal/commit/16ade8253f26200246abb5ab24d17e18216e7a11.patch";
+      sha256 = "sha256-N6YqfcOUWeaJXVE9RUo1dzulxqIY5Q/UygPnZHau3Lc=";
     })
   ];
 
@@ -229,8 +229,8 @@ stdenv.mkDerivation (finalAttrs: {
     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/v3.7.0/autotest/gdrivers/bag.py#L61
-    export BUILD_NAME=fedora
+    # https://github.com/OSGeo/gdal/blob/v3.9.0/autotest/gdrivers/bag.py#L54
+    export CI=1
   '';
   nativeInstallCheckInputs = with python3.pkgs; [
     pytestCheckHook
diff --git a/pkgs/development/libraries/pdal/default.nix b/pkgs/development/libraries/pdal/default.nix
index 86d976531cb3..edaf281c65bc 100644
--- a/pkgs/development/libraries/pdal/default.nix
+++ b/pkgs/development/libraries/pdal/default.nix
@@ -87,6 +87,12 @@ stdenv.mkDerivation (finalAttrs: {
   doCheck = true;
 
   disabledTests = [
+    # Failing due to GDAL 3.9 change in coordinates precision.
+    # See: https://github.com/PDAL/PDAL/issues/4403
+    # This test should be re-enabled once https://github.com/PDAL/PDAL/pull/4411
+    # is merged !
+    "pdal_io_ogr_writer_test"
+
     # Tests failing due to TileDB library implementation, disabled also
     # by upstream CI.
     # See: https://github.com/PDAL/PDAL/blob/bc46bc77f595add4a6d568a1ff923d7fe20f7e74/.github/workflows/linux.yml#L81
diff --git a/pkgs/development/python-modules/geopandas/default.nix b/pkgs/development/python-modules/geopandas/default.nix
index 021292f8c4ac..e4b958d42461 100644
--- a/pkgs/development/python-modules/geopandas/default.nix
+++ b/pkgs/development/python-modules/geopandas/default.nix
@@ -3,6 +3,7 @@
   stdenv,
   buildPythonPackage,
   fetchFromGitHub,
+  fetchpatch,
   pytestCheckHook,
   pythonOlder,
   setuptools,
@@ -29,6 +30,20 @@ buildPythonPackage rec {
     hash = "sha256-FBhPcae8bnNnsfr14I1p22VhoOf9USF9DAcrAqx+zso=";
   };
 
+  patches = [
+    # GDAL 3.9 compat for boolean array in shp
+    (fetchpatch {
+      url = "https://github.com/geopandas/geopandas/commit/f1be60532bed31cb410ce4db2da6b733bc8713c9.patch";
+      sha256 = "sha256-DZhC7sSOki0XTcojSRvVVSlsnYnxCw/Ee7vHBmDCsbA=";
+    })
+
+    # GDAL 3.9 compat for boolean array in shp for fiona
+    (fetchpatch {
+      url = "https://github.com/geopandas/geopandas/commit/1e08422d8aee4877752047a8a08f41e3a67188f2.patch";
+      sha256 = "sha256-SpNqe7jL1rA79YhhSUfEzt30plt56Tux5v1h7IHp31I=";
+    })
+  ];
+
   build-system = [ setuptools ];
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/rasterio/default.nix b/pkgs/development/python-modules/rasterio/default.nix
index 158394a3b331..d7ab45fd4732 100644
--- a/pkgs/development/python-modules/rasterio/default.nix
+++ b/pkgs/development/python-modules/rasterio/default.nix
@@ -99,6 +99,12 @@ buildPythonPackage rec {
   disabledTests = [
     # flaky
     "test_outer_boundless_pixel_fidelity"
+
+    # Failing with GDAL 3.9.
+    # Fixed in https://github.com/rasterio/rasterio/commit/24d0845e576158217f6541c3c81b163d873a994d
+    # Re-enable in next rasterio update.
+    "test_create_sidecar_mask"
+    "test_update_tags"
   ] ++ lib.optionals stdenv.isDarwin [ "test_reproject_error_propagation" ];
 
   pythonImportsCheck = [ "rasterio" ];