Salinity intrusion in coastal systems is mainly controlled by freshwater inflows. However, extreme events like drought, low-pressure storms, and longer-term sea level rise can exacerbate the landward salt migration and threaten economic infrastructure and ecological health. Along the eastern seaboard of the United States, approximately 13 million people rely on the water resources of the Delaware River basin. Salinity intrusion is actively managed through river discharge targets to suppress the propagation of the salt front (∼0.52 daily averaged psu line). The purpose of this study is to examine the mechanisms controlling the location of the salt front in the Delaware Bay estuary using a calibrated three-dimensional hydrodynamic model, the Coupled Ocean Atmosphere Wave and Sediment Transport modeling system. This study explored how river discharge, tidal motions, interactions with bathymetric and topographic features, and meteorological events affected the location of the salt front. The model was forced with tides, subtidal water levels, bulk atmospheric conditions, and waves. Compared with the observationally derived location of the salt front line, the model captured the major dynamics throughout the year and performed particularly well during times of low discharge, when salinity intruded up estuary at a constant rate of 0.4 km/day. The daily average salt front moved almost 16 km (10 mi) within a neap-spring tidal cycle, and low-pressure storm systems were found to move the daily averaged salt front by 13–16 km in one event.