In this paper we develop a model to estimate nitrogen loading to watersheds and receiving waters, and then apply the model to gain insight about sources, losses, and transport of nitrogen in groundwater moving through a coastal watershed. The model is developed from data of the Waquoit Bay Land Margin Ecosystems Research project (WBLMER), and from syntheses of published information. The WBLMER nitrogen loading model first estimates inputs by atmospheric deposition, fertilizer use, and wastewater to surfaces of the major types of land use (natural vegetation, turf, agricultural land, residential areas, and impervious surfaces) within the landscape. Then, the model estimates losses of nitrogen in the various compartments of the watershed ecosystem. For atmospheric and fertilizer nitrogen, the model allows losses in vegetation and soils, in the vadose zone, and in the aquifer. For wastewater nitrogen, the model allows losses in septic systems and effluent plumes, and it adds further losses that occur during diffuse transport within aquifers. The calculation of losses is done separately for each major type of land cover, because the processes and loss rates involved differ for different tesserae of the land cover mosaic. If groundwater flows into a freshwater body, the model adds a loss of nitrogen for traversing the freshwater body and then subjects the surviving nitrogen to losses in the aquifer. The WBLMER model is developed for Waquoit Bay, but with inputs for local conditions it is applicable to other rural to suburban watersheds underlain by unconsolidated sandy sediments. Model calculations suggest that the atmosphere contributes 56%, fertilizer 14%, and wastewater 27% of the nitrogen delivered to the surface of the watershed of Waquoit Bay. Losses within the watershed amount to 89% of atmospheric nitrogen, 79% of fertilizer nitrogen, and 65% of wastewater nitrogen. The net result of inputs to the watershed surface and losses within the watershed is that wastewater becomes the largest source (48%) of nitrogen loads to receiving estuaries, followed by atmospheric deposition (30%) and fertilizer use (15%). The nitrogen load to estuaries of Waquoit Bay is transported primarily through land parcels covered by residential areas (39%, mainly via wastewater), natural vegetation (21%, by atmospheric deposition), and turf (16%, by atmospheric deposition and fertilizers). Other land covers were involved in lesser throughputs of nitrogen. The model results have implications for management of coastal landscapes and water quality. Most attention should be given to wastewater disposal within the watershed, particularly within 200 m of the shore. Rules regarding setbacks of septic system location relative to shore and nitrogen retention ability of septic systems, will be useful in control of wastewater nitrogen loading. Installation of multiple conventional leaching fields or septic systems in high-flow parcels could be one way to increase nitrogen retention. Control of fertilizer use can help to a modest degree, particularly for optional uses such as lawns situated near shore. Conservation of parcels of accreting natural vegetation should be given high priority, because these environments effectively intercept atmospheric deposition. Areas upgradient from freshwater bodies should be given low priority in plans to control nitrogen loading, because ponds intercept much of the nitrogen transported from upgradient.