Phosphorus (P) deficiency often occurs in paddy fields due to its high fixation, and low solubility and mobility in soils, especially under water stress. Available soil P and plant P uptake could be improved through the application of zeolite. However, little is known about the impact of zeolite on P uptake in rice under water stress. A two-year lysimetric experiment using a split-split plot design investigated the effects of zeolite (0 or 15 t ha−1) and P (0 or 60 kg ha−1) applications on water use, P uptake, and grain yield in rice under two irrigation management systems (continuous flooding irrigation (CF) and improved alternate wetting and drying irrigation (IAWD)). Both irrigation systems produced equivalent effective panicles and grain yield. Compared with CF, IAWD reduced water use and aboveground P uptake and improved water-use efficiency (WUE) in rice. The applications of zeolite or P alone increased grain yield, WUE, soil available P, and stem, leaf, and panicle P concentration, and aboveground P uptake, but had no significant effect on water use. The enhanced grain yield induced by zeolite was related to the increase in aboveground P uptake. The zeolite application enhanced NH4+–N retention in the topsoil and prevented NO3−–N from leaching into deeper soil layers. Moreover, Zeolite made lower rates of P fertilizer possible in paddy fields, with benefits for remaining P supplies and mitigating pollution due to excessive P. These results suggest that the combined application of zeolite and P under improved AWD regime reduced water use, improved P uptake and grain yield in rice, and alleviated environment risk.