In estuaries, phosphorus (P) and nitrogen (N) inputs generally control freshwater and saltwater primary production, respectively. Improved wastewater P removal and a P-detergent ban in the late 1980s decreased P loading to the nutrient over-enriched Neuse River Estuary, NC, without a contemporaneous reduction in N loading. This led to a decrease in upstream freshwater phytoplankton production and a reduction in nuisance algal blooms. While this nutrient management approach appeared to be effective in reducing the symptoms of freshwater eutrophication, it may have also diminished the upstream algal N filter, promoting N enrichment, relative to P enrichment, and eutrophication of the more saline downstream N-limited waters. Recent N controls implemented by the State of North Carolina should help address the problem. These findings underscore the need for watershed- and basin-scale, dual nutrient (N and P) reduction strategies that consider the entire freshwater--marine continuum as well as hydrologic variability (e.g., hurricanes, floods, droughts) when formulating long-term controls of estuarine eutrophication.