Continental shelves around the globe are hosts to vast reservoirs of offshore freshened groundwater. These systems show considerable complexity, often as a function of the geological heterogeneity. Data needed to characterise these systems are often sparse, and numerical models rely on generalized simplifications of the geological environment. In order to improve our understanding of these systems, it is necessary to implement modelling approaches that can produce large-scale geologically representative models using sparse data. We present an interdisciplinary stochastic modelling workflow incorporating borehole data, 2D depth-migrated seismic profiles, seismic attributes, and prior knowledge of the depositional setting. We generate a conditioned Gaussian field of porosity on the New Jersey shelf. We also perform a petrophysical conversion to a corresponding permeability distribution. The model dimensions are 134 km × 69 km × 1.7 km, with an adjustable resolution that can be adapted for process-based models of flow and solute transport. The integrated approach successfully translates small-scale porosity variations to a shelf-scale model that honors key characteristics of the New Jersey shelf wave-dominated depositional environment. The model was generated using open-source packages. All data and code to reproduce the complete workflow are provided along with this study so the model can be reproduced at any resolution for further studies of continental shelf processes offshore New Jersey.