Stream water exports of nutrients and pollutants to water bodies integrate internal and external watershed processes that vary in both space and time. In this paper, we explore nitrate (NO3) fluxes for the 326 km2 mixed-land use Fall Creek watershed in central New York for 1972–2005, and consider internal factors such as changes in land use/land cover, dynamics in agricultural production and fertilizer use, and external factors such as atmospheric deposition. Segmented regression analysis was applied independently to dormant and growing seasons for three portions of the period of record, which indicated that stream water NO3 concentrations increased in both dormant and growing seasons from the 1970s to the early 1990s at all volumes of streamflow discharge. Dormant season NO3 concentrations then decreased at all flow conditions between the periods 1987–1993 and 1994–2005. Results from a regression-based stream water loading model (LOADEST) normalized to mean annual concentrations showed annual modeled NO3 concentration in stream water increased by 34% during the 1970s and 1980s (from 1.15 to 1.54 mg l−1), peaked in about 1989, and then decreased by 29% through 2005 (to 1.09 mg l−1). Annual precipitation had the strongest correlation with stream water NO3 concentrations (r = −0.62, P = 0.01). Among land use factors, corn production for grain was the variable most highly correlated to stream water NO3 concentrations (r = 0.53, P = 0.01). The strongest associative trend determined using Chi-squared Automatic Interaction Detection (CHAID) was found between stream water NO3 concentrations and N-equivalence of dairy production (Bonferroni adjusted P value = 0.0003). Large increases in dairy production were coincident with declining nitrate concentrations over the past decade, which suggest that dairy management practices may have improved in the watershed. However, because dairy production in the Fall Creek watershed has been fueled by large increases in feed imports, the environmental costs of feed production have likely been externalized to other watersheds.