Most beneficial management practices (BMPs) recommended for reducing nutrient losses from agricultural land have been established and tested in temperate and humid regions. Previous studies on the effects of these BMPs in cold-climate regions, especially at the small watershed scale, are rare. In this study, runoff and water quality were monitored from 1999 to 2008 at the outlets of two sub-watersheds in the South Tobacco Creek watershed in Manitoba, Canada. Five BMPs—a holding pond below a beef cattle overwintering feedlot, riparian zone and grassed waterway management, grazing restriction, perennial forage conversion, and nutrient management—were implemented in one of these two sub-watersheds, beginning in 2005. We determined that > 80% of the N and P in runoff at the outlets of the two sub-watersheds were lost in dissolved forms, approximately 50% during snowmelt events and 33% during rainfall events. When all snowmelt- and rainfall-induced runoff events were considered, the five BMPs collectively decreased Total N (TN) and Total P (TP) exports in runoff at the treatment sub-watershed outlet by 41% and 38%, respectively. The corresponding reductions in flow-weighted mean concentrations (FWMCs) were 43% for TN and 32% for TP. In most cases, similar reductions in exports and FWMCs were measured for both dissolved and particulate forms of N and P, and during both rainfall and snowmelt-induced runoff events. Indirect assessment suggests that retention of nutrients in the holding pond could account for as much as 63% and 57%, respectively, of the BMP-induced reductions in TN and TP exports at the treatment sub-watershed outlet. The nutrient management BMP was estimated to have reduced N and P inputs on land by 36% and 59%, respectively, in part due to the lower rates of nutrient application to fields converted from annual crop to perennial forage. Overall, even though the proportional contributions of individual BMPs were not directly measured in this study, the collective reduction of nutrient losses from the five BMPs was substantial.