Irrigation water rights and their governance structures constitute the foundation of local water institutions and profoundly influence water resource allocations, irrigated agricultural productivity and other consumptive water uses in the arid climate zones. This article explores the regional structures of irrigation water rights and water governance and empirically analyses the priority effects of water rights on irrigated agriculture at the micro level in Idaho, an arid and semiarid state in the western United States. We integrate a unique data set of water rights and water supplies with agricultural features and environmental characteristics into our empirical analysis. Results indicate that seniority in water resources allocation has significant, positive effects on both the average crop revenue and crop water use efficiency. Local water rights structures differ significantly in seniority and water sources from region to region. In response to the heterogeneity in local water rights structures, the aforementioned effect of allocative priority of water rights on average crop revenue per hectare and crop water productivity varies significantly, reaching up to an 87% difference, when measured across regions. In addition, the priority effects of water rights are nonlinear, which reflects the influence of historical patterns of water rights establishment on water institutions to date.