Subwatersheds within the Great Lakes “Priority Watersheds” were targeted by the Great Lakes Restoration Initiative (GLRI) to determine the effectiveness of the various best management practices (BMPs) from the U.S. Department of Agriculture-Natural Resources Conservation Service National Conservation Planning (NCP) Database. A Soil and Water Assessment Tool (SWAT) model is created for Alger Creek, a 50 km2 tributary watershed to the Saginaw River in Michigan. Monthly calibration yielded very good Nash–Sutcliffe efficiency (NSE) ratings for flow, sediment, total phosphorus (TP), dissolved reactive phosphorus (DRP), and total nitrogen (TN) (0.90, 0.79, 0.87, 0.88, and 0.77, respectively), and satisfactory NSE rating for nitrate (0.51). Two-year validation results in at least satisfactory NSE ratings for flow, sediment, TP, DRP, and TN (0.83, 0.54, 0.73, 0.53, and 0.60, respectively), and unsatisfactory NSE rating for nitrate (0.28). The model estimates the effect of BMPs at the field and watershed scales. At the field-scale, the most effective single practice at reducing sediment, TP, and DRP is no-tillage followed by cover crops (CC); CC are the most effective single practice at reducing nitrate. The most effective BMP combinations include filter strips, which can have a sizable effect on reducing sediment and phosphorus loads. At the watershed scale, model results indicate current NCP BMPs result in minimal sediment and nutrient reductions (<10%).