Nitrogen isotope ratios (δN) in juvenile winter flounder, Pseudopleuronectes americanus, were used to examine changes in nitrogen inputs to several Rhode Island, USA estuarine systems. Fish were collected over two three-year periods with a ten-year interval between sampling periods (2002-2004 and 2012-2014). During that interval numerous changes to nutrient management practices were initiated in the watersheds of these estuarine systems including the upgrade of several major wastewater treatment facilities that discharge to Narragansett Bay, which significantly reduced nitrogen inputs. Following these reductions, the δN values of flounder in several of the systems decreased as expected; however, isotope ratios in fish from upper Narragansett Bay significantly increased. We believe that low δN values measured in 2002-2004 were related to concentration-dependent fractionation at this location. Increased δN values measured between 2012 and 2014 may indicate reduced fractionation or that changes in wastewater treatment processes altered the nitrogen isotopic ratios of the effluents.