Simulating discontinuous phenomena such as shock waves and wave breaking during wave propagation and run-up has been a challenging task for wave modeller. This requires a robust, accurate, and efficient numerical implementation. In this paper, we propose a two-dimensional numerical model for simulating wave propagation and run-up in shallow areas. We implemented numerically the 2-dimensional Shallow Water Equations (SWE) on a staggered grid by applying the momentum conserving approximation in the advection terms. The numerical model is named MCS-2d. For simulations of wet–dry phenomena and wave run-up, a method called thin layer is used, which is essentially a calculation of the momentum deactivated in dry areas, i.e., locations where the water thickness is less than the specified threshold value. Efficiency and robustness of the scheme are demonstrated by simulations of various benchmark shallow flow tests, including those with complex bathymetry and wave run-up. The accuracy of the scheme in the calculation of the moving shoreline was validated using the analytical solutions of Thacker 1981, N-wave by Carrier et al., 2003, and solitary wave in a sloping bay by Zelt 1986. Laboratory benchmarking was performed by simulation of a solitary wave run-up on a conical island, as well as a simulation of the Monai Valley case. Here, the embedded-influxing method is used to generate an appropriate wave influx for these simulations. Simulation results were compared favorably to the analytical and experimental data. Good agreement was reached with regard to wave signals and the calculation of moving shoreline. These observations suggest that the MCS method is appropriate for simulations of varying shallow water flow.