Agricultural practices act as an ecological filter of weeds, selecting those more adapted to the agrosystem. The stress conditions due to cultivation preparations shape the weed community, influencing the productive performance of the crops. Among these practices, irrigation can directly affect the establishment of some weeds, and a better-adapted community can intensify the degree of interference with agricultural cultures. This study aims to evaluate the changes in the weed community caused by two irrigation systems (high and low rates of water application) over three onion seasons, and how these changes affect the yield and efficiency of irrigated onion. The γ-, α-, and β diversity pf weeds was altered by onion cultivation over the three seasons. The irrigation system with a higher water supply (micro-sprinkler) favored diversity and weed richness, especially during the second cultivation year, compared to the system with water restriction (drip irrigation). Under the micro-sprinkler system, transition of the weed communities among years took place gradually. The higher level of stress created by drip management stimulated the dominance of Digitaria horizontalis. Non-control of weeds at 12 and 24 days after crop emergence reduced the onion crop yield. Besides that, this reduction in productivity indices was aggravated by the greater weed diversity under the micro-sprinkler system (high water supply). Under drip irrigation (low water supply), dominance intensify the competition of the weed community on the onion crop yield. The density of weeds and C4 species negatively affected onion growth under drip irrigation.