Nitrogen (N) supply by atmospheric deposition, wastewater, and fertilizers controls estuarine eutrophication. In New England, atmospheric N loads recently decreased by 50% and land-derived contributions rose about 80%, owing to national-scale emission controls and local urban development. The decrease in atmospheric deposition was large enough to balance increases in land-derived N loads, so total N loads to Waquoit Bay estuaries in Cape Cod did not change significantly between 1990 and 2014. Unchanged N regimes were corroborated by finding no differences in estuarine nutrient concentrations and macrophyte biomass between pre-2005 and in 2015. Coastal zones, subject to reasonably rapid changes in global and local driver variables, will require that assessment and management of eutrophication include adaptive strategies that capture effects of changing baselines. Management initiatives will be constrained by spatial scale of driver variables: local efforts may address wastewater and fertilizer N sources, but atmospheric sources require national or international attention.