diff --git a/pkgs/development/python-modules/pygeos/default.nix b/pkgs/development/python-modules/pygeos/default.nix
deleted file mode 100644
index ebb90ee9fef7..000000000000
--- a/pkgs/development/python-modules/pygeos/default.nix
+++ /dev/null
@@ -1,48 +0,0 @@
-{
-  lib,
-  buildPythonPackage,
-  fetchPypi,
-  python,
-  geos_3_11,
-  pytestCheckHook,
-  cython_0,
-  numpy,
-}:
-
-buildPythonPackage rec {
-  pname = "pygeos";
-  version = "0.14";
-  format = "setuptools";
-
-  src = fetchPypi {
-    inherit pname version;
-    hash = "sha256-MPvBf2SEQgC4UTO4hfz7ZVQbh3lTH270+P5GfT+6diM=";
-  };
-
-  nativeBuildInputs = [
-    geos_3_11 # for geos-config
-    cython_0
-  ];
-
-  propagatedBuildInputs = [ numpy ];
-
-  # The cythonized extensions are required to exist in the pygeos/ directory
-  # for the package to function. Therefore override of buildPhase was
-  # necessary.
-  buildPhase = ''
-    ${python.pythonOnBuildForHost.interpreter} setup.py build_ext --inplace
-    ${python.pythonOnBuildForHost.interpreter} setup.py bdist_wheel
-  '';
-
-  nativeCheckInputs = [ pytestCheckHook ];
-
-  pythonImportsCheck = [ "pygeos" ];
-
-  meta = with lib; {
-    description = "Wraps GEOS geometry functions in numpy ufuncs";
-    homepage = "https://github.com/pygeos/pygeos";
-    changelog = "https://github.com/pygeos/pygeos/blob/${version}/CHANGELOG.rst";
-    license = licenses.bsd3;
-    maintainers = teams.geospatial.members;
-  };
-}
diff --git a/pkgs/top-level/python-aliases.nix b/pkgs/top-level/python-aliases.nix
index 206b08ad509b..9cfa1e4fafa5 100644
--- a/pkgs/top-level/python-aliases.nix
+++ b/pkgs/top-level/python-aliases.nix
@@ -389,6 +389,7 @@ mapAliases ({
   pyramid_multiauth = pyramid-multiauth; # added 2023-08-24
   pyreadability = readability-lxml; # added 2022-05-24
   pyres = throw "pyres has been removed, since it is abandoned and broken"; # added 2023-06-20
+  pygeos = throw "pygeos has been removed, since it was merged with shapely 2.0"; # added 2024-05-26
   pyRFC3339 = pyrfc3339; # added 2024-01-07
   pyroute2-core = throw "pyroute2 migrated back to a single package scheme in version 0.7.1"; # added 2022-07-16
   pyroute2-ethtool = throw "pyroute2 migrated back to a single package scheme in version 0.7.1"; # added 2022-07-16
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 2134664da533..e131624f2999 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -11052,8 +11052,6 @@ self: super: with self; {
 
   pygeoip = callPackage ../development/python-modules/pygeoip { };
 
-  pygeos = callPackage ../development/python-modules/pygeos { };
-
   pygetwindow = callPackage ../development/python-modules/pygetwindow { };
 
   pygit2 = callPackage ../development/python-modules/pygit2 { };