Nitrogen (N) loading to estuaries has become a major concern for coastal planners. As urban development on coastal watershed continues, estuaries and bays are becoming more eutrophic, and cascading effects are being felt at every trophic level. Managers and stakeholders need to have a suite of effective management tools that can be applied to coastal watersheds to minimize the effects of eutrophication. We applied an N loading model and an estuarine loading model to examine the effectiveness of a suite of potential management options that could be implemented in Waquoit Bay, Cape Cod, Massachusetts. This estuarine system is a case study in which we can explore the relative potential effectiveness of decreasing inputs from wastewater and fertilizer-derived N, diverting nitrogenous runoff from impervious surfaces, altering zoning ordinances, preserving forested tracts of land as well as freshwater and saltwater wetlands, harvesting macroalgae, dredging estuary channels, and exterminating waterfowl. From a combination of simulation results, assessment of the magnitude of loads from different sources, and through different land covers, and the additional consideration of feasibility we identified management options with high, intermediate, and low potential effectiveness. Improvement of septic system performance, use of zoning regulations, preservation of forested tracts and freshwater bodies, and conservation of salt marshes emerged as the most promising avenues to manage N loads in our system. Installation of wastewater treatment plants, controlling fertilizer use, and harvesting macroalgae would potentially have intermediate success. Diversion of runoff from impervious surfaces, dredging, and extermination of waterfowl show little promise at reducing N loads. These conclusions potentially set priorities for decision-makers charged with the management of Waquoit Bay. The same procedures applied to another watershed-estuary system with different land covers and different estuarine features may differ. Evaluation studies like this need to be done for any particular site, since the watershed-estuary coupling and the loads delivered to the receiving estuary could differ. The Waquoit Bay case study provides an example of a protocol that leads to identification of the most promising management options.