Whole Farm Planning was instituted and monitored over a 5-year period within the Graywood Gully sub-watershed of Conesus Lake, NY (USA). An array of agricultural Best Management Practices (BMPs) (strip cropping, fertilizer reduction, tiling, manure disposal practices, etc.) were simultaneously introduced to determine the impact of a concentrated management effort on nutrient and soil loss from one watershed within the Conesus Lake catchment. During the study period, significant decreases in winter concentrations of dissolved and particulate fractions, including total phosphorus (TP), soluble reactive phosphorus (SRP), total Kjeldahl nitrogen (TKN), and nitrate (NO₃) but not total suspended solids (TSS), were observed. These decreases may or may not be attributed to cessation of manuring practices. Three years into the study, an opportunity existed to test the responsiveness of the watershed to the curtailment of a single BMP — winter manure application to fields. We field-tested the hypothesis that a change in winter manure applications would impact dissolved and particulate fractions in stream water draining this watershed. We found that the water quality of Graywood Gully is very responsive to winter manure application on environmentally sensitive portions of the sub-watershed. With the short-term resumption of manure application, TP, SRP, TKN, and NO₃ concentrations rose dramatically in stream water; elevated phosphorus concentrations persisted over a 5-week period. Total suspended solids, however, were not elevated after short-term manure application. Factors that affected these results were slope of the land, application of manure over snow and during a snowfall, warm air and soil temperatures, and possibly tile drainage of snowmelt water. Managers of agricultural systems must recognize that phosphorus losses from the watershed during the nongrowing season may detrimentally affect nuisance population of algae in lakes during the summer.