BOUSS-2D is a comprehensive numerical model for simulating the propagation and transformation of waves in coastal regions and harbors based on a time-domain solution of Boussinesq-type equations. The governing equations are uniformly valid from deep to shallow water and can simulate most of the phenomena of interest in the nearshore zone and harbor basins including shoaling/refraction over variable topography, reflection/diffraction near structures, energy dissipation due to wave breaking and bottom friction, cross-spectral energy transfer due to nonlinear wave-wave interactions, breaking-induced longshore and rip currents, wave-current interaction and wave interaction with porous structures. Many processes at inlets and harbors can be studied using BOUSS-2D.