Water-rights driven surface-water allocations for irrigated agriculture can be simulated using the farm process for MODFLOW-2000. This paper describes and develops a model, which simulates routed surface-water deliveries to farms limited by streamflow, equal-appropriation allotments, or a ranked prior-appropriation system. Simulated diversions account for deliveries to all farms along a canal according to their water-rights ranking and for conveyance losses and gains. Simulated minimum streamflow requirements on diversions help guarantee supplies to senior farms located on downstream diverting canals. Prior appropriation can be applied to individual farms or to groups of farms modeled as “virtual farms” representing irrigation districts, irrigated regions in transboundary settings, or natural vegetation habitats. The integrated approach of jointly simulating canal diversions, surface-water deliveries subject to water-rights constraints, and groundwater allocations is verified on numerical experiments based on a realistic, but hypothetical, system of ranked virtual farms. Results are discussed in light of transboundary water appropriation and demonstrate the approach’s suitability for simulating effects of water-rights hierarchies represented by international treaties, interstate stream compacts, intrastate water rights, or ecological requirements.