Across most of the World's coastal zone there has been a geographic transition from naturally vegetated to human-altered land covers, both agricultural and urban. This transition has increased the nitrogen loads to coastal watersheds, and from watersheds to receiving estuaries. We modeled the nitrogen entering the watershed of Waquoit Bay, Massachusetts, and found that as the transition took place, nitrogen loads to watersheds increased from 1938 to 1990. The relative magnitude of the contribution by wastewater, fertilizers, and atmospheric deposition depends on the land cover mosaics of a watershed. Atmospheric deposition was the major input to the watershed surface during this period, but because of different rates of loss within the watershed. wastewater became the major source of nitrogen flowing from the watershed to the receiving estuaries. Atmospheric deposition prevails in watersheds dominated by natural vegetation such as forests, but wastewater may become a dominant source in watersheds where urbanization increases. Increased nitrogen loads resulting from conversion of natural to human-altered watershed surfaces create eutrophication of receiving waters, with attendant changes in water quality, and marked shifts in the flora and food webs of the affected estuaries. Management efforts for restoration of eutrophied estuaries require maintenance of forested land, and control of wastewater and fertilizer inputs, the major terms in most affected places subject to local management. Wastewater and fertilizer nitrogen derive from within the watershed, which means local measures may effectively be used to control eutrophication of receiving waters.