Organic cropping systems are characterized by soil-disturbance events that can be diversified over years through crop rotations and within seasons by varying planting dates. The Farming Systems Project at Beltsville, MD, USA, is a long-term experiment that includes three organic rotations, corn (Zea mays L.)–soybean [Glycine max (L.) Merr.], corn–soybean–wheat (Triticum aestivum L.), and corn–soybean–wheat–alfalfa (Medicago sativa L.). Analysis of weed presence and cover over the first 18 yr of this experiment revealed that the tall, erect annual broadleaf weeds smooth pigweed (Amaranthus hybridus L.), common lambsquarters (Chenopodium album L.), horseweed (Erigeron canadensis L.), jimsonweed (Datura stramonium L.), and/or velvetleaf (Abutilon theophrasti Medik.) were most prominent in corn and soybean. Generally, these species exhibited traits adapted to the disturbance regimes, nutrient availability, crop environment and duration, and local meteorological conditions associated with the summer annual corn and soybean crops. Abundance of A. hybridus, D. stramonium, and A. theophrasti were controlled primarily by rotation diversity, whereby presence and cover of these species were highest in the short corn–soybean rotation and lowest in the longer rotations that had more diverse seasonal soil-disturbance regimes. Early-season temperature was the primary factor controlling C. album presence and cover, which were higher at lower temperatures associated with earlier planting dates. Higher early-season precipitation was the primary factor associated with higher presence of annual grass species. The relative abundance of species in organic corn and soybean was determined primarily by the diversity of crops and disturbance operations in rotation, the timing of spring tillage and planting, and annual meteorological conditions driving emergence periodicity.