The U.S Geological Survey (USGS) compiled and analyzed existing hydrologic and water-quality data from over 200 stream and estuary stations of the Abemarle-Pamlico estuarine system (A/P) to identify long-term temporal and spatial trends. The dataset included seven stations of the USGS National Stream Quality Accounting Network, two stations of the National Atmospheric Precipitation Deposition monitoring network, stations of the N.C. Department of Natural Resources and Community Development, and stations from 25 reports by individual investigators. Regression-residuals analysis, the seasonal Kendall's Tau test for trends, and graphical analysis using annual box plots were employed to determine trends. Profound change has occurred in the water quality of the A/P area over the last 30 years. Analysis of water-quality data upstream from the estuaries indicates increases of discharge-adjusted values of specific conductance, alkalinity, phosphorous, hardness, chloride, and dissolved solids. In the estuaries, pH is increasing except in the Pamlico River, where it is decreasing. There is a generalized decrease in suspended inorganic material in the system. Salinities are decreasing for sections of the Pamlico River, and increasing for parts of Albemarle Sound. Nitrogen concentrations are decreasing except in the Pamlico River, where they are increasing. Phosphorus concentrations are increasing in the Pamlico River and decreasing elsewhere. Annual average data show that nitrogen is the limiting nutrient in the Neuse and Pamlico Rivers. Phosphorus is limiting in the rest of the area. Chlorophyll-a levels are increasing in parts of the Neuse and Pamlico Rivers and decreasing in parts of the Chowan River. To evaluate the effect of basin characteristics on water quality, linear correlation was used. Agricultural crop variables produced the most correlations with water-quality data. Fertilizer usage had little detectable relation to water quality in the study area. In the section of the Pamlico River near Aurora, relations between employment, road mileages, and water quality indicated effects of development in the area.