In this study we investigated the impact of climate change on nutrient loading in the Cannonsville Reservoir watershed of the New York City (NYC) water supply system where management practices have reduced nutrient inputs in the last 25 years. A modified version of the SWAT hydrological and water quality model (SWAT-HS) that had been previously tested and verified for streamflow and phosphorus for this watershed was calibrated for nitrate to estimate contributions from point and nonpoint sources. Model simulations show that forests that occupy 64% of the watershed area contribute the greatest proportion of nitrate at 39%, while pastures that are in close proximity to streams and runoff generating areas contribute the greatest proportion of total nitrogen at 34%. Point sources contribute less than 5% of the annual nitrate load. Stream export accounts for only about 23% of the annual total N input to the watershed from anthropogenic sources, suggesting significant storage or loss from the landscape. We assumed stationary land use and management practices to assess the change in nutrient loading from baseline (2001–2010) to middle of the century (2051–2060) period due to a change in climate. Results indicated no change to moderate increase in the annual loading of dissolved forms of nutrients (N and P) whereas particulate forms of nutrients and sediment loadings are projected to increase due to an increase in the frequency and magnitude of large storm events. A seasonal shift in streamflow due to warmer winter temperatures, greater amounts of precipitation falling as rain, and earlier melting of snowpack may play an important role in controlling the seasonal pattern of nutrient loading. The methodology used in this study can be adapted in other watersheds to estimate the relative importance and partition contributions from various nonpoint sources to water quality, and to investigate the impacts of climate change.