Freshwater is limited in the semi-arid Arequipa region in Southern Peru that is home to more than 1.3 million people, agricultural and industrial sectors. To address water demand, eight reservoirs and more than 200 km of water diversion tunnels and canals have been implemented in the Quilca and Camaná river basins, resulting in severely modified hydrology and interconnection of the two basins. The Soil and Water Assessment Tool (SWAT) was used to simulate the current hydrological status and potential alternative management scenarios for the two interconnected basins. Simulation challenges include scarcity of data on soil and land cover to run SWAT, which was addressed by developing publicly available regional soil and land cover databases. A representation of water infrastructure required a complex model structure incorporating point sources to represent water transfers and reservoir outflows and water withdrawals at 17 locations. The developed model is used to provide a comprehensive understanding of water availability in the region under current and alternate scenarios for water regulation. The impact of current water infrastructure on minimum streamflow is explored in the Quilca and Camaná river basins. Results were shared with the local water authorities and the public via an online tool called HidroAQP to support water allocation and related water resource decisions.