Offshore freshened groundwater reservoirs occur on continental shelves in several regions of the world. Their origins are an active area of research, however, models often rely on simplified geometrical representations of subsurface geology. The New Jersey shelf hosts an extensive multi-layered freshened groundwater system that previous paleo-reconstructions have not reproduced. In this numerical case-study, we aim to characterize the New Jersey shelf system in the context of a geologically representative heterogeneous model. Our model combines sequence stratigraphic interpretation of 2D depth migrated seismic lines and a stochastic facies distribution with petrophysical properties of four boreholes. We employ a stochastic approach to generate both high and low onshore-offshore connectivity scenarios. The study considers a 58 000-year recharge period for the subaerially exposed shelf transect, followed by the marine transgression from 12 000 years ago until today. The results show that the lowstand period drove sufficient freshwater emplacement that can explain most of the present-day observations. The highest rates of recharge occurred during the periods of most rapid sea-level fall. Simulated scenarios indicate that topographically driven flow of meteoric recharge via surface-connected pathways is the key emplacement mechanism. Surviving freshwater systems exhibit lateral variability in salinity due to downward fingering of saline pore fluid. Freshwater preserved from the Last Glacial Maximum may extend up to 100 km from the coastline. The results also suggest that cyclical flushing and re-salinization of shelf sediments during glacial-interglacial cycles is an asymmetrical process, promoting freshwater storage over geological time scales.