diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 157f45f3f2a9..758f84c1a099 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -3345,19 +3345,43 @@ in {
 
   python-mapnik = buildPythonPackage rec {
     name = "python-mapnik-${version}";
-    version = "3.0.13";
+    version = "3.0.16";
 
     src = pkgs.fetchFromGitHub {
       owner = "mapnik";
       repo = "python-mapnik";
       rev = "v${version}";
-      sha256 = "0biw9bfkbsgfyjihyvkj4abx9s9r3h81rk6dc1y32022rypsqhkp";
+      sha256 = "1gqs4kvmjawdgl80j0ab5r8y0va9kw0rvwix3093xsv4hwd00lcc";
     };
 
     disabled = isPyPy;
     doCheck = false; # doesn't find needed test data files
-    buildInputs = with pkgs;
-      [ boost cairo harfbuzz icu libjpeg libpng libtiff libwebp mapnik proj zlib ];
+    preBuild = let
+      pythonVersion = with stdenv.lib.versions; "${major python.version}${minor python.version}";
+    in ''
+      export BOOST_PYTHON_LIB="boost_python${pythonVersion}"
+      export BOOST_THREAD_LIB="boost_thread"
+      export BOOST_SYSTEM_LIB="boost_system"
+    '';
+    buildInputs = with pkgs; [
+        (boost.override {
+          enablePython = true;
+          inherit python;
+        })
+        (mapnik.override {
+          inherit python;
+          boost = (boost.override { enablePython = true; inherit python; });
+        })
+        cairo
+        harfbuzz
+        icu
+        libjpeg
+        libpng
+        libtiff
+        libwebp
+        proj
+        zlib
+      ];
     propagatedBuildInputs = with self; [ pillow pycairo ];
 
     meta = with stdenv.lib; {