A process-based numerical modeling system is utilized for predicting littoral sand transport. The intent is to examine conditions slightly more complex than linear waves impinging upon a plane beach. Two factors that we examine are wave skewness and longshore varying bathymetry. An empirical model is used for calculating the skewed bottom wave orbital velocity. The advection of sediment due to the skewed wave velocity is larger and in the direction of the waves, opposite to the results with sinusoidal wave velocities, due to the increase in the bottom shear stress under the wave crests. The model system is also applied to bathymetry containing beach cusps. When the wave field has relatively weak longshore wave power, the currents and the littoral transport exhibit significant longshore variability, thereby altering the overall mean littoral transport.