Nutrient, herbicide, and sediment loading from agricultural fields cause environmental and economic damage. Nutrient leaching and runoff pollution can lead to eutrophication and impaired drinking water resources, while soil erosion reduces water quality and agronomic productivity. Increased cropping system diversification has been proposed to address these problems. We used the ArcSWAT model and long-term Iowa field experimental measurements to estimate eutrophication and erosion impacts of three crop rotation systems under two weed management regimes. Rotations were comprised of 2-year corn-soybean, 3-year corn-soybean-oat/clover, and 4-year corn-soybean-oat/alfalfa-alfalfa systems. All were managed with conventional or low herbicide applications. Total N and P runoff losses were up to 39% and 30% lower, respectively, in the more diverse systems than the 2-year corn-soybean system, but NO3--N leaching losses were unaffected by cropping system. Diversification reduced erosion losses up to 60%. The 3- and 4-year systems maintained or increased crop yields and net returns relative to the 2-year conventional system. Reductions in herbicide use intensity generally did not affect nutrient and sediment losses nor crop yields and profitability. These results indicate that diversifying the corn-soybean rotation that dominates the central United States could reduce water nutrient contamination and soil erosion while maintaining farm productivity and profitability.