Biogeochemical couplings between land and coastal waters are increasingly altered by land cover changes forced by accumulation of human uses of watersheds. In particular, human activities increase nitrogen loads to receiving waters. Definitions of forcings require estimation of external nitrogen sources and evaluation of the effects on the roles of different land covers, retention within watersheds, and net exports to the sea. One powerful example of change in N loads is the effect of urban development on the watershed and concentrations of inorganic nitrogen in the water of Great South Bay (GSB), New York. We defined land uses, delimited subwatersheds emptying into GSB, and estimated nitrogen loads to subwatersheds and from these to receiving waters. Wastewater-derived nitrogen was the dominant source to watershed surfaces (55%), with lesser amounts added by atmospheric deposition to land (31%) and fertilizer use (15%). About 77% of nitrogen entering the watershed was retained within the watershed, so that despite land use changes, the watershed furnished a substantial water quality subsidy, preventing enrichment of GSB. This high within-watershed retention is similar to rates observed elsewhere and was to a significant degree linked to areas of natural vegetation. About 50% of total nitrogen that entered GSB was of wastewater origin; only 16% was contributed by atmospheric deposition on land, 26% by direct atmospheric deposition on GSB, and 7% by use of fertilizer on land. In addition, the direct atmospheric deposition onto GSB amounted to 44% of the land-derived load, within ranges affecting other estuaries.

GSB is low on the range of eutrophication of estuaries. Within-watershed retention is still high, but land cover changes manage to force enough throughput of land-derived nitrogen—particularly wastewater nitrogen—to enrich coastal receiving waters. As land cover further shifts away from natural vegetation, eutrophication of GSB, and coastal receiving waters in general, will increase.