Submarine groundwater discharge (SGD) is a small portion of the global water budget, but a potentially large contributor to coastal nutrient budgets due to high concentrations relative to stream discharge. A numerical groundwater flow model of the Inland Bays Watershed, Delaware, USA, was developed to identify the primary hydrogeologic factors that affect groundwater discharge rates and transit times to streams and bays. The distribution of groundwater discharge between streams and bays is sensitive to the depth of the water table below land surface. Higher recharge and reduced hydraulic conductivity raised the water table and increased discharge to streams relative to bays compared to the Reference case (in which 66% of recharge is discharged to streams). Increases to either factor decreased transit times for discharge to both streams and bays compared to the Reference case (in which mean transit times are 56.5 and 94.3 years, respectively), though sensitivity to recharge is greater. Groundwater-borne nitrogen loads were calculated from nitrogen concentrations measured in discharging fresh groundwater and modeled SGD rates. These loads combined with long SGD transit times suggest groundwater-borne nitrogen reductions and estuarine water quality improvements will lag decades behind implementation of efforts to manage nutrient sources. This work enhances understanding of the hydrogeologic controls on and uncertainties in absolute and relative rates and transit times of groundwater discharge to streams and bays in coastal watersheds.