A time-domain Boussinesq model was applied to modeling wave interference and its effects on nearshore circulation in San Francisco Bar and the adjacent Ocean Beach, CA. The model predicted the wave interference phenomena caused by the ebb shoal, with interference scales consistent with the Radar observation. Model results reveal that small-scale fingering structures in the wave height distribution result from wave interference and are persistent with nodal lines unchanged with time. Nearshore circulation predicted by the model shows small-scale flow structures tied with the wave modulation patterns. However, the small-scale modulation in the wave field seems not to generate alongshore variation in wave setup at similar scales. Therefore, in a large-scale view, the alongshore currents predicted by the Boussinesq model still keep the general features shown in a wave-averaged model, such as the flow divergence caused by the pressure gradient force associated with the alongshore variation of wave setup. The time-domain Boussinesq model predicted the spatial variability of wave-induced processes. The alongshore-varying wave breakers caused by wave interference are the source of the vorticity generation, inducing energetic vortex eddies nearshore.