It is imperative to understand the interconnectedness of water use and hydrological impacts for water policy design underlying varying hydrological conditions across space and over time. However, such analysis remains difficult, constrained by the lack of appropriate modeling tools that fully integrate water policies, water use, and hydrological processes with high spatiotemporal resolutions. To address this challenge, this study proposes a distributed policy design scheme featuring spatially variable and temporally dynamic policies for conjunctive surface water‐groundwater management in large river basins. A fully integrated modeling framework is developed to tightly couple (a) an agent‐based model for farmers' water use under distributed water policies and (b) a physically based hydrological model for surface water‐groundwater processes. The modeling framework is applied to the Heihe River Basin to assess water use and hydrological impacts under distributed water policies. By using the distributed policy scheme to adjust a water policy (e.g., groundwater tax) across space and over time, we found that hydrological outcomes can be improved without adversely reducing agricultural water supply. For example, by shifting the implementation of a high groundwater tax from dry to wet years, a rise of the water table by 0.28 m (0.03–0.95 m across different irrigation districts) can be achieved while the total water supply is maintained at a similar level. Furthermore, hydrological externality effects among nearby districts can be explicitly identified and quantified based on assessments of spatially varying water policies. This study highlights the need for water policy design to consider spatiotemporal variations in the physical hydrological system.