Breakwaters are a common shoreline protection structure, often trapping sediment as the incoming wave energy is reduced. Quantifying the dynamics and volume of these sediment sinks within a coastal system is an important step toward understanding the sediment budget for a particular coastal area. This study examines the volume of sediment deposited within the breakwater enclosed Point Judith Harbor of Refuge (Rhode Island, United States of America (USA)) in the late 19th century using seismic reflection profiles, bathymetric mapping, and isotopic analysis of core sediment. Geophysical profiles show a district seismic facies up to 4 m thick above the ravinement surface, particularly in the western and central portion of the harbor. Century-scale bathymetric changes revealed shoaling of a similar magnitude, and isotopic data support the deposition of this sediment package within the 20th century. The total volume of sediment within the harbor exceeds 5.0 × 106 m3, with an estimated sand volume of 3.6 × 106 m3. The results show that the harbor is a substantial sediment sink for the Rhode Island South Shore and provide the basis for future studies of the sediment budget for this shoreline.