A long-term, field-scale study in southern Manitoba, Canada, was used to identify the critical factors controlling yearly transport of nitrogen (N) and phosphorus (P) by snowmelt runoff. Flow monitoring and water sampling for total and dissolved N and P were performed at the edge of field. The flow-weighted mean concentrations and loads of N and P for the early (the first half of yearly total volume of snowmelt runoff), late (the second half of yearly total volume of snowmelt runoff), and yearly snowmelt runoff were calculated as response variables. A data set of management practices, weather variables, and hydrologic variables was generated and used as predictor variables. Partial least squares regression analysis indicated that critical factors affecting the water chemistry of snowmelt runoff depended on the water quality variable and stage of runoff. Management practices within each year, such as nitrogen application rate, number of tillage passes, and residue burial ratio, were critical factors for flow-weighted mean concentration of N, but not for P concentration or nutrient loads. However, the most important factors controlling nutrient concentrations and loads were those related to the volume of runoff, including snow water equivalent, flow rate, and runoff duration. The critical factors identified for field-scale yearly snowmelt losses provide the basis for modeling of nutrient losses in southern Manitoba and potentially throughout areas with similar climate in the northern Great Plains region, and will aid in the design of effective practices to reduce agricultural nonpoint nutrient pollution in downstream waters.