Six small, predominantly agricultural (>70%) watersheds in the Conesus Lake catchment of New York State, USA, were selected to test the impact of Best Management Practices (BMPs) on mitigation of nonpoint nutrient sources and soil loss from farms to downstream aquatic systems. Over a 5-year period, intensive stream water monitoring and analysis of covariance provided estimates of marginal means of concentration and loading for each year weighted by covariate discharge. Significant reductions in total phosphorus, soluble reactive phosphorus, nitrate, total Kjeldahl nitrogen, and total suspended solids concentration and flux occurred by the second year and third year of implementation. At Graywood Gully, where Whole Farm Planning was practiced and a myriad of structural and cultural BMPs were introduced, we observed the greatest percent reduction (average = 55.8%) and the largest number of significant reductions in analytes (4 out of 5). Both structural and cultural BMPs were observed to have profound effects on nutrient and soil losses. Where fields were left fallow or planted in a vegetative type crop, reductions, especially in nitrate, were observed. Where structural implementation occurred, reductions in total fractions were particularly evident. Where both were applied, major reductions in nutrients and soil occurred. After 5 years of management, nonevent and event concentrations of total suspended solids in streams draining agricultural watersheds were not significantly different from those in a relatively “pristine/reference” watershed. This was not the case for nutrients.