The St. Jones watershed of central Delaware is critically impacted by development. To understand the effects of these changes on nitrogen loading of the estuary, an all-encompassing model of the nitrogen sources and transport methods had to be developed. Using numerous GIS coverages and the ArcView GIS-based BASINS model the surface hydrology was simulated, and by transferring the spatial data output to the groundwater model MODFLOW the subsurface hydrology was predicted. Surface and subsurface nitrogen loadings based on land use, sewered areas, point sources, and other factors spatially compiled through the GIS along with atmospheric deposition led to the development of a watershed loading equation that can be easily modified to estimate the impacts of future development.