Weeds have acquired evolutionary adaptations to the diverse crop and weed management strategies used in cropping systems. Therefore, changes in crop production practices such as conventional to organic systems, tillage-based to no-till systems, and diversity in crop rotations can result in differences in weed community composition that have management implications. A study was carried out to understand the weed community dynamics in a long-term alternative cropping systems study at Scott, SK, Canada. Long-term (18-yr) weed community composition data in wheat (Triticum aestivum L.) in ORG (organic), RED (reduced-input, no-till), and HIGH (high-input, conventional tillage) systems with three levels of crop rotation diversity, LOW (low diversity), DAG (diversified annual grains), and DAP (diversified annuals and perennials), were used to study the effect of different cropping systems and the effect of environment (random temporal effects) on residual weed community composition using the principal response curve (PRC) technique. The interaction between cropping systems and year-to-year random environmental changes was found to be the predominant factor causing fluctuations in weed community composition. Furthermore, the single most predominant factor influencing the weed composition was year-to-year random changes. Organic systems clearly differed from the two conventional systems in most years and had more diverse weed communities compared with the two conventional systems. The two conventional systems exhibited similar weed composition in most years. In this study, the use of the PRC method allowed capture of the real temporal dynamics reflected in the cropping systems by time interaction. This study further concludes that moving from a tillage-based, high-input conventional system to a no-till, reduced-input system did not cause significant changes in the weed community composition throughout the time period, but diversity in organic systems was high, probably due to increased occurrence of some difficult to control species.