Cover crops (CCs) play an important role in integrated weed management. Data necessary to evaluate the role of CCs in weed management at the watershed scale with topographic positions are lacking. We evaluated the effects of cereal rye and hairy vetch CCs on weed suppression at different topographic positions (shoulder, backslope, and footslope) at a watershed scale. Watersheds with a CC treatment followed a crop rotation of corn–cereal rye–soybean–hairy vetch, whereas watersheds without a CC (no-CC) had a crop rotation of corn–winter fallow–soybean–winter fallow. A negative relationship was present between CCs and weed biomass at the shoulder, backslope, and footslope topographic landscape positions, with R2 values of 0.40, 0.48, and 0.50, respectively. In 2016, a cereal rye CC reduced weed biomass 46% to 50% at footslope and shoulder positions compared to no CC. In 2018, a cereal rye CC reduced weed biomass between 52% and 85% at all topographic positions in CC treatment watersheds compared to no-CC watersheds. Hairy vetch in 2017 reduced weed biomass 62% to 72% at footslope and shoulder topographic positions in CC watersheds compared to no-CC. The C:N ratio of weed biomass in CC treatment watersheds was generally higher compared to watersheds without CCs. In this study, several significant interactions were found between the topographic positions and CC treatments. Cover crop–induced weed suppression at different topographic positions can lead to developing better site-specific weed control strategies. Therefore, CC interactions with topography, weed germination potential, and the role of soil moisture at the watershed scale should be further evaluated.