Nutrient concentrations and loads and Escherichia coli (E. coli) densities were studied in 2005 and from 2008 through 2011 in water-quality samples from tributaries of the Niantic River Estuary in southeastern Connecticut. Data from a water-quality survey of the base flow of subbasins in the watershed in June 2005 were used to determine the range of total nitrogen concentrations (0.09 to 2.4 milligrams per liter), instantaneous loads (less than 1 to 62 pounds per day) and the yields of total nitrogen ranging from 0.02 to 11.2 pounds per square mile per day (less than 1 to 7.2 kilograms per hectare per year) from basin segments. Nitrogen yields were positively correlated with the amount of developed land in each subbasin. Stable isotope measurements of nitrate (δ¹⁵N) and oxygen (δ¹⁸O) ranged from 3.9 to 9.4 per mil and 0.7 to 4.1 per mil, respectively, indicating that likely sources of nitrate in base flow are soil nitrate and ammonium fertilizers, sewage or animal waste, or a mixture of these sources. Continuous streamflow and monthly water-quality sampling, with additional storm event sampling, were conducted at the three major tributaries (Latimer Brook, Oil Mill Brook, and Stony Brook) of the Niantic River from October 2008 through September 2011. Samples were analyzed for nitrogen and phosphorus constituents and E. coli densities. Total freshwater discharge from these tributaries, which is reduced by upstream withdrawals, ranged from 25.9 to 37.8 million gallons per day. Total nitrogen and phosphorus concentrations generally were low, with the mean values below the U.S. Environmental Protection Agency recommended nutrient concentration values of 0.71 milligram per liter and 0.031 milligram per liter, respectively. Total nitrogen was predominantly in the form of total ammonia plus organic nitrogen at the Oil Mill Brook and Stony Brook sites and in the form of nitrate at Latimer Brook. Annual total nitrogen loads that flowed into the Niantic River estuary from the three major tributaries, calculated with the Load Estimator computer program, ranged from 41,400 to 60,700 pounds, with about 52 to 59 percent of the load as total ammonia plus organic nitrogen. Total phosphorus loads ranged from 1,770 to 3,540 pounds per year. Yields of total nitrogen were highest from Latimer Brook, with the range from the three tributaries between 1,100 and 2,720 pounds per square mile per year. Total phosphorus yields ranged from 52 to 185 pounds per square mile per year. The geometric means of E. coli densities in samples from the three Niantic River tributaries were less than the State of Connecticut water-quality standard of 126 colony-forming units per 100 milliliters; however, individual samples from all three tributaries had densities as high as 2,400 to 2,900 colony-forming units per 100 milliliters. High densities of E. coli were more likely to be present in samples collected during wet weather events.