Since the mid 1990s, the Atlantic and Gulf Coast regions have experienced a dramatic increase in the number of hurricane landfalls. In eastern North Carolina alone, eight hurricanes have affected the coast in the past 9 years. These storms have exhibited individualistic hydrologic, nutrient, and sediment loading effects and represent a formidable challenge to nutrient management aimed at reducing eutrophication in the Pamlico Sound and its estuarine tributaries. Different rainfall amounts among hurricanes lead to variable freshwater and nutrient discharge and variable nutrient, organic matter, and sediment enrichment. These enrichments differentially affected physical and chemical properties (salinity, water residence time, transparency, stratification, dissolved oxygen), phytoplankton primary production, and phytoplankton community composition. Contrasting ecological responses were accompanied by changes in nutrient and oxygen cycling, habitat, and higher trophic levels, including different direct effects on fish populations. Floodwaters from the two largest hurricanes, Fran (1996) and Floyd (1999), exerted multi-month to multi-annual effects on hydrology, nutrient loads, productivity, and biotic composition. Relatively low rainfall coastal hurricanes like Isabel (2003) and Ophelia (2005) caused strong vertical mixing and storm surges, but relatively minor hydrologic and nutrient effects. Both hydrologic loading and wind forcing are important drivers and must be integrated with nutrient loading in assessing short-term and long-term ecological effects of these storms. These climatic forcings cannot be managed but should be considered in the development of water quality management strategies for these and other large estuarine ecosystems faced with increasing frequencies and intensities of hurricane activity.