The Neuse River and Estuary, a major tributary of the second largest estuary on the United States mainland, historically has sustained excessive blooms of algae and toxic dinoflagellates, hypoxia, and fish kills. Previous attempts have been made to use short-term databases of 2-3 years, or data sets from infrequent (monthly) sampling, to assess whether nutrient inputs to the Neuse are increasing and supporting higher algal production. These previous efforts also have relied on single-point-determined flow velocity data, at upstream sites remote from the estuary, to estimate the volume of flow in quantifying nutrient loading to the estuary. We completed a five-year study of the Neuse, including a comparative inventory of nutrients to the watershed from point sources and from concentrated animal operations (CAOs) as recent nonpoint sources, as well as an intensive assessment of water quality over time in the mesohaline estuary. Estimates of nutrient loads were based on volume of flow data from shore-to-shore transect cross sections, taken with a boat-mounted acoustic Doppler current profiler at the westernmost edge of the estuary. Alemán