diff --git a/pkgs/development/python-modules/graph-tool/default.nix b/pkgs/development/python-modules/graph-tool/default.nix
index 5dc014626300..f455258ea14b 100644
--- a/pkgs/development/python-modules/graph-tool/default.nix
+++ b/pkgs/development/python-modules/graph-tool/default.nix
@@ -2,14 +2,16 @@
   buildPythonPackage,
   lib,
   fetchurl,
+  fetchpatch,
   stdenv,
 
-  boost,
+  boost189,
   cairomm,
   cgal,
   expat,
-  gmp,
+  fontconfig,
   gobject-introspection,
+  graphviz,
   gtk3,
   llvmPackages,
   matplotlib,
@@ -21,11 +23,22 @@
   python,
   scipy,
   sparsehash,
+  zstandard,
   gitUpdater,
 }:
 
 let
-  boost' = boost.override {
+  boost' = boost189.override {
+    patches = [
+      # required to build against Clang >= 21 (https://github.com/boostorg/lexical_cast/pull/87)
+      # TODO: drop when upgrading to Boost >= 1.90
+      (fetchpatch {
+        name = "Reduce-dependency-on-Boost.TypeTraits-now-that-C-11-.patch";
+        url = "https://github.com/boostorg/lexical_cast/commit/8fc8a19931c8cb452400af907959fdacbbdd8ec1.patch";
+        relative = "include";
+        hash = "sha256-OO39ejR+I5ufjqinrMJ6HgjTE7Ph+XBu50PqcIKaIQo=";
+      })
+    ];
     enablePython = true;
     inherit python;
   };
@@ -33,50 +46,77 @@ in
 buildPythonPackage rec {
   pname = "graph-tool";
   version = "2.98";
-  format = "other";
+  pyproject = false;
 
   src = fetchurl {
     url = "https://downloads.skewed.de/graph-tool/graph-tool-${version}.tar.bz2";
     hash = "sha256-7vGUi5N/XwQ3Se7nX+DG1+jwNlUdlF6dVeN4cLBsxSc=";
   };
 
-  postPatch = ''
+  postPatch =
     # remove error messages about tput during build process without adding ncurses
-    substituteInPlace configure \
-      --replace-fail 'tput setaf $1' : \
-      --replace-fail 'tput sgr0' :
-  '';
+    ''
+      substituteInPlace configure \
+        --replace-fail 'tput setaf $1' : \
+        --replace-fail 'tput sgr0' :
+    ''
+    +
+    # hardcode path to graphviz library to avoid find_library, which would require setting LD_LIBRARY_PATH
+    ''
+      substituteInPlace src/graph_tool/draw/graphviz_draw.py \
+        --replace-fail \
+          'ctypes.util.find_library("gvc")' \
+          '"${lib.getLib graphviz}/lib/libgvc${stdenv.hostPlatform.extensions.sharedLibrary}"'
+    '';
 
-  configureFlags = [
-    "--with-python-module-path=$(out)/${python.sitePackages}"
-    "--with-boost-libdir=${boost'}/lib"
-    "--with-cgal=${cgal}"
-  ];
+  configureFlags =
+    lib.mapAttrsToList (lib.withFeatureAs true) {
+      boost-libdir = "${lib.getLib boost'}/lib";
+      cgal = lib.getDev cgal;
+      python-module-path = "$(out)/${python.sitePackages}";
+    }
+    ++
+      lib.optionals stdenv.cc.isGNU
+        # enable GCC's link-time optimizer in order to reduce compilation time and memory usage during compilation
+        # https://graph-tool.skewed.de/installation.html#memory-requirements-for-compilation
+        # https://git.skewed.de/count0/graph-tool/-/issues/798#note_5626
+        [ "MOD_CXXFLAGS=-flto" ];
 
   enableParallelBuilding = true;
 
-  build-system = [ pkg-config ];
+  nativeBuildInputs = [ pkg-config ];
 
   # https://graph-tool.skewed.de/installation.html#manual-compilation
-  dependencies = [
+  buildInputs = [
     boost'
     cairomm
     cgal
     expat
-    gmp
-    gobject-introspection
-    gtk3
-    matplotlib
     mpfr
-    numpy
-    pycairo
-    pygobject3
-    scipy
     sparsehash
   ]
   ++ lib.optionals stdenv.cc.isClang [ llvmPackages.openmp ];
 
-  pythonImportsCheck = [ "graph_tool" ];
+  dependencies = [
+    gtk3
+    matplotlib
+    numpy
+    pycairo
+    pygobject3
+    scipy
+    zstandard
+  ];
+
+  propagatedNativeBuildInputs = [ gobject-introspection ];
+
+  preInstallCheck =
+    # avoid warnings about Matplotlib and Fontconfig configuration issues
+    ''
+      export HOME=$(mktemp -d)
+      export FONTCONFIG_FILE=${fontconfig.out}/etc/fonts/fonts.conf
+    '';
+
+  pythonImportsCheck = [ "graph_tool.all" ];
 
   passthru.updateScript = gitUpdater {
     url = "https://git.skewed.de/count0/graph-tool";
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 59cd56ae87ec..434a4fc41ee5 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -6444,7 +6444,7 @@ self: super: with self; {
 
   granian = callPackage ../development/python-modules/granian { };
 
-  graph-tool = callPackage ../development/python-modules/graph-tool { inherit (pkgs) cgal; };
+  graph-tool = callPackage ../development/python-modules/graph-tool { inherit (pkgs) cgal graphviz; };
 
   grapheme = callPackage ../development/python-modules/grapheme { };