diff --git a/pkgs/development/libraries/geos/3.9.nix b/pkgs/development/libraries/geos/3.9.nix
deleted file mode 100644
index 70cfa917993b..000000000000
--- a/pkgs/development/libraries/geos/3.9.nix
+++ /dev/null
@@ -1,34 +0,0 @@
-{
-  lib,
-  stdenv,
-  fetchurl,
-  cmake,
-  testers,
-}:
-
-stdenv.mkDerivation (finalAttrs: {
-  pname = "geos";
-  version = "3.9.5";
-
-  src = fetchurl {
-    url = "https://download.osgeo.org/geos/geos-${finalAttrs.version}.tar.bz2";
-    hash = "sha256-xsmu36iGT7RLp4kRQIRCOCv9BpDPLUCRrjgFyGN4kDY=";
-  };
-
-  nativeBuildInputs = [ cmake ];
-
-  enableParallelBuilding = true;
-
-  passthru.tests.pkg-config = testers.testMetaPkgConfig finalAttrs.finalPackage;
-
-  meta = with lib; {
-    description = "C++ port of the Java Topology Suite (JTS)";
-    mainProgram = "geos-config";
-    homepage = "https://trac.osgeo.org/geos";
-    license = licenses.lgpl21Only;
-    pkgConfigModules = [ "geos" ];
-    maintainers = with lib.maintainers; [
-      willcohen
-    ];
-  };
-})
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index a30a122bbfa3..3983c112f00e 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -989,6 +989,7 @@ mapAliases {
   gdmd = throw "gdmd has been removed from Nixpkgs, as it depends on GDC which was removed"; # Added 2025-08-08
   gdome2 = throw "'gdome2' has been removed from nixpkgs, as it is umaintained and obsolete"; # Added 2024-12-29
   geocode-glib = throw "'geocode-glib' has been removed, as it was unused and used outdated libraries"; # Added 2025-04-16
+  geos_3_9 = throw "geos_3_9 has been removed from nixpkgs. Please use a more recent 'geos' instead."; # Added 2025-09-21
   geos_3_11 = throw "geos_3_11 has been removed from nixpkgs. Please use a more recent 'geos' instead."; # Added 2024-11-29
   gfbgraph = throw "'gfbgraph' has been removed as it was archived upstream and unused in nixpkgs"; # Added 2025-04-20
   gfortran48 = throw "'gfortran48' has been removed from nixpkgs"; # Added 2024-09-10
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index b4396829efcb..0aa6e787e188 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -7524,8 +7524,6 @@ with pkgs;
 
   geos = callPackage ../development/libraries/geos { };
 
-  geos_3_9 = callPackage ../development/libraries/geos/3.9.nix { };
-
   gettext = callPackage ../development/libraries/gettext { };
 
   gdalMinimal = gdal.override {