Increasing crop rotation diversity while reducing herbicide applications may maintain effective weed control while reducing freshwater toxicity. To test this hypothesis, we applied the model USEtox 2.0 to data from a long-term Iowa field experiment that included three crop rotation systems: a 2-year corn-soybean sequence, a 3-year corn-soybean-oat/red clover sequence, and 4-year corn-soybean-oat/alfalfa-alfalfa sequence. Corn and soybean in each rotation were managed with conventional or low-herbicide regimes. Oat, red clover, and alfalfa were not treated with herbicides. Data from 2008-2015 showed that use of the low-herbicide regime reduced freshwater toxicity loads by 81-96%, and that use of the more diverse rotations reduced toxicity and system dependence on herbicides by 25-51%. Mean weed biomass in corn and soybean was <25 kg ha-1 in all rotation × herbicide combinations except the low-herbicide 3-year rotation, which contained ∼110 kg ha-1 of weed biomass. Corn and soybean yields and net returns were as high or higher for the 3- and 4-year rotations managed with the low-herbicide regime as for the conventional-herbicide 2-year rotation. These results indicate that certain forms of cropping system diversification and alternative weed management strategies can maintain yield, profit, and weed suppression while delivering enhanced environmental performance.