This meta‐analysis evaluated the impact of agro‐ecological practices and water management techniques on lowland rice yield and water productivity (WP). A total of 573 observations were collected from 56 articles that met specific criteria from 445 publications. Five water management practices were assessed: continuous flooding (CF), soil saturation (SS), moderate (AWDm) and severe (AWDs) alternate wetting and drying, and the aerobic rice system (ARS). The response ratios (RRs) of yield and WP were compared for crop management, soil fertility, weed control and evaporation. The integration of agro‐ecological practices such as short‐cycle rice varieties, crop rotation, organic nutrient application and mechanical weeding with water management led to similar yields across CF, SS, AWDm and AWDs, with ARS consistently yielding the lowest yields. However, medium‐ and long‐cycle varieties under AWDs experienced yield losses of 11 and 13%, respectively. Mineral fertilizer combined with AWDs resulted in a 14% lower yield than did CF. Mechanical weeding increased the rice yield and WP by 10 and 10% in SS, and only WP by 35% in AWDs, whereas chemical weeding decreased the yield by 13% in AWDs. Crop rotation enhanced yield and WP by 13 and 12%, respectively, under AWDm compared to that under CF. WP was greater under AWDs (36%) and AWDm (12%) than under CF.