Evolution equations are derived for weakly nonlinear, multi-frequency and directional surface gravity waves propagating from deep to shallow water over weakly two-dimensional bottom topography. A uniform transition from cubic resonances in deep–intermediate water (Stokes regime) to quadratic near resonances in shallow water (Boussinesq regime) is obtained by extending the ordered solution to include additional higher-order terms for the bound wave components. The model assumes a leading-order, alongshore-uniform bottom with a two-dimensional depth perturbation that is incorporated through a Taylor series expansion of the bottom boundary condition. Numerical implementations of the model and comparisons to experimental data are presented that demonstrate the model's ability to describe: (i) cubic wave–wave interactions in deep–intermediate water depth; (ii) harmonic generation over a one-dimensional submerged obstacle; (iii) harmonic generation over two-dimensional topography.