The paper presents a numerical model of the two-dimensional enhanced Boussinesq equations to simulate wave transformations in the near-shore region. The finite element-based discretisation over unstructured mesh with triangular elements uses mixed linear and quadratic shape functions. The domain integrals are calculated analytically. The model is extended to study flow through porous structures using Darcy velocity, with the energy dissipation within the porous medium modelled through additional laminar and turbulent resistance terms. A single set of empirical constants gives accurate prediction for various stone sizes and porosity. This paper reports the model development and its validation using existing experimental studies. Application of the model is demonstrated by studying the interaction between ship-generated waves in a narrow channel and the porous walls of the channel. © Springer Nature Singapore Pte Ltd. 2019.