Conservation management practices such as reduced tillage, fertilizer management, and buffer strips are well-established means by which to control erosion and nutrient losses from fields planted in annual row crops. However, agricultural systems which include perennial plant cover, such as the perennial forages found in grazing systems, may represent an alternative way to reduce these losses. In this study, management intensive rotational grazing (MIRG) was tested as a means by which to improve water quality on highly vulnerable row crop land, compared to more traditional conservation management schemes in the south branch of the Root River Watershed (a karst-influenced watershed in Southeastern Minnesota). The effects of both sets of alternative scenarios were evaluated with a watershed-based modeling approach using the Soil and Water Assessment Tool. Alternative conservation management practices included conservation tillage, cover crops, and filter strips. Conversion of row crop production to management-intensive rotational grazing of beef cattle was selected to occur on 2.6% of the total watershed area. Both the conservation management practices and land use changes were targeted to reduce contributions of sediment and phosphorus (P) loads from cropped upland areas. Watershed-wide implementation of all conservation management practices resulted in the greatest reductions in sediment (52%) and total P (28%) loads from upland crop areas, but had the largest land area requirements to achieve these results. Cover crops or filter strips on areas of high slope also showed large cumulative reductions across the watershed and also had the greatest reductions per-unit treated area of all conservation management practices. However, changing land use from row crop production to pasture for grazing was most effective at reducing total sediment and P loads on those acres changed, reducing sediment and P by greater than 85% on targeted areas. Simulation results indicate that utilizing alternative conservation management practices or MIRG, when targeted to areas of steeper slope (greater than 4%), could appreciably reduce sediment and P loads in this watershed, with limited reductions in row crop agriculture acreage.