diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 3e2e1d18..717fd520 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -286,12 +286,20 @@ jobs:
           name: data
           path: ~/.cache/mhkit
 
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: sudo apt-get install -y libhdf5-dev libnetcdf-dev
+
       - name: Update and install packages
         shell: bash -l {0}
         run: |
           python -m pip install --upgrade pip wheel
           pip install -e  ".[all,dev]"
 
+      - name: Reinstall h5py and netCDF4 with system libraries
+        if: runner.os == 'Linux'
+        run: "pip install --force-reinstall --no-binary=:all: h5py netCDF4"
+
       - name: Install setuptools for Python 3.12
         if: matrix.python-version == '3.12'
         run: pip install setuptools
@@ -417,12 +425,18 @@ jobs:
           name: data
           path: ~/.cache/mhkit
 
+      - name: Install system dependencies
+        run: sudo apt-get install -y libhdf5-dev libnetcdf-dev
+
       - name: Install MHKiT with optional dependency
         run: |
           python -m pip install --upgrade pip
           pip install "mhkit[${{ matrix.module }}]"
           pip install pytest
 
+      - name: Reinstall h5py and netCDF4 with system libraries
+        run: "pip install --force-reinstall --no-binary=:all: h5py netCDF4"
+
       - name: Run tests for ${{ matrix.module }}
         env:
           MPLBACKEND: Agg