Human encroachment and development on coastlines have led to greater amounts of armoring of shorelines. Breakwaters are a common feature along coastlines, which are used to dampen wave energy and protect shorelines from flash floods or overwash events. Although common, their effects on sediment transport and marsh geomorphology are poorly understood. To address this gap, our study quantifies the effects of breakwaters on sediment transport and marsh evolution under different wave regimes using Delft3D-SWAN, a dynamic geomorphodynamic numerical model. Model configurations used the same numerical domain, but scenarios had different sediments, waves, tides, basin slopes and breakwater distances from the shoreline to explore how waves and tidal currents shape coastal margins. Model results suggested breakwaters were responsible for an average wave damping between 10–50%, proportional to the significant wave height across all modeled scenarios. Shear stress at the beginning of the marsh and the volume of sediment deposited at the end of the simulation (into the marsh behind the breakwater) increased on average between 20–40%, proportional to the slope and distance of the breakwater from the shoreline. Sediment trapping, defined as the ratio between the volume of sediment housed into the salt marsh behind and away from the breakwater, was found to be less than 1 from most model runs. Study results indicated that breakwaters are advantageous for wave breaking to protect shorelines from the wave’s energy, however, they might also be an obstacle for sediment transport, negatively affecting nourishment processes, and, consequently, impeded long-term salt marsh survival. Identifying a balance between waves dampening and shoreline nourishment should be considered in the design and implementation of these structures.