The replacement of flood‐irrigation systems by drip‐irrigation technology has been widely promoted with the aim of a more sustainable use of freshwater resources in irrigated agriculture. However, evidence for an irrigation efficiency paradox emphasizes the need to improve our understanding of the impacts of irrigation transformations on water resources. Here, we developed a distributed hydrological modeling approach to investigate the spatiotemporal effect of flood and drip irrigation on groundwater recharge. The approach recognizes differences in the water balance resulting from the localized application of water in surface drip‐irrigated fields and the more extensive application of water in flood irrigation. The approach was applied to the semi‐arid Mediterranean region of Valencia (Spain) and calibrated using a multi‐objective framework. Multiple process scales were addressed within the framework by considering the annual evaporative index, monthly groundwater level dynamics, and daily soil moisture dynamics. Daily simulations from 1994 to 2015 suggested that, in our hydroclimatic conditions, (a) annual recharge is strongly related to annual rainfall, which had a four times higher impact on recharge than the type of irrigation practice, (b) flood‐irrigated recharge tends to exceed drip‐irrigated recharge by 10% at annual time scales, (c) however, recharge response to a particular precipitation event is smaller in flood irrigation than in drip irrigation, and (d) 8–18 rainfall events could generate more than half of the annual recharge in drip and flood irrigation, respectively. Our results highlight the importance of understanding the hydrological dynamics under different irrigation practices for supporting irrigation infrastructure policies. Key Points We developed a modeling approach to simulate the impacts of a transition from flood to drip irrigation on basin scale groundwater recharge Annual recharge was strongly related to annual rainfall, but to a much smaller extent to irrigation practice Sensitivity of daily recharge to single precipitation events was stronger in drip irrigation than in flood irrigation