Three major hypotheses were examined in this study: (1) the density of summer annual weeds is reduced in crop rotation systems that include winter wheat compared to those with strictly summer annual crops, (2) the integration of a red clover in cropping systems reduces weed seedbank densities, and (3) changes in weed seedbanks due to crop rotation system have greater impact on future crops that are managed with cultivation alone, compared to those managed with herbicides. To test these hypotheses, five 3-yr rotation sequences were examined in central New York state: continuous field corn (FC); field corn with red clover (FC CL); field corn–oats–wheat (FC/O/W); sweet corn–peas–wheat (SC/P/W), and SC/P/W with red clover (SC/P/W CL). In the fourth year, sweet corn, snap beans, and cabbage were planted in subplots with three levels of weed management as sub-subplots: cultivation alone, reduced-rate herbicides (1/2×), and full-rate herbicides (1×). The trial was carried out in two separate cycles, from 1997 to 2000 (cycle 1) and from 1998 to 2001 (cycle 2). Crop rotations with strictly summer annual crops (FC) did not result in consistently higher weed seedbank densities of summer annual weeds compared to rotations involving winter wheat (FC/O/W; SC/P/W; SC/P/W CL). Integration of red clover in continuous field corn resulted in higher weed seedbanks (cycle 1) or emergence (cycle 2) of several summer annual weeds compared to field corn alone. In contrast, integration of red clover in the SC/P/W rotation led to a 96% reduction in seedbank density of winter annuals in cycle 1, although this effect was not detected in cycle 2. Observed changes in weed seedbank density and emergence due to crop rotation resulted in increased weed biomass in the final year in only one case (sweet corn, cycle 2), and did not result in detectable differences in crop yields. In contrast, final year weed management had a strong effect on weed biomass and yield; cultivation alone resulted in yield losses for sweet corn (32 to 34%) and cabbage (0 to 7%), but not snap beans compared to either 1/2× or 1× herbicides.