Eutrophication is a serious water quality problem in estuaries receiving increasing anthropogenic nutrient loads. Managers undertaking nutrient-reduction strategies aimed at controlling estuarine eutrophication are faced with the challenge that upstream freshwater segments often are phosphorus (P)-limited, whereas more saline downstream segments are nitrogen (N)-limited. Management also must consider climatic (hydrologic) variability, which affects nutrient delivery and processing. The interactive effects of selective nutrient input reductions and climatic perturbations were examined in the Neuse River Estuary (NRE), North Carolina, a shallow estuary with more than a 30-year history of accelerated nutrient loading and water quality decline. The NRE also has experienced a recent increase in Atlantic hurricanes and record flooding, which has affected hydrology and nutrient loadings. The authors examined the water quality consequences of selective nutrient (P but not N) reductions in the 1980s, followed by N reductions in the 1990s and an increase in hurricane frequency since the mid-1990s. Selective P reductions decreased upstream phytoplankton blooms, but increased downstream phytoplankton biomass. Storms modified these trends. In particular, upstream annual N and P concentrations have decreased during the elevated hurricane period. Increased flushing and scouring from storms and flooding appear to have enhanced nutrient retention capabilities of the NRE watershed. From a management perspective, one cannot rely on largely unpredictable changes in storm frequency and intensity to negate anthropogenic nutrient enrichment and eutrophication. To control eutrophication along the hydrologically variable freshwater-marine continuum, N and P reductions should be applied adaptively to reflect point-source-dominated drought and non-point-source-dominated flood conditions.