Decades of urbanization have created sprawling, complex, and vulnerable cities, half of which are located in water-scarce areas. With the looming effects of climate change, including increasing droughts and water shortages, there is an urgent need to better understand how urbanization impacts the water cycle at city scale. Impervious surfaces disrupt the natural flow of water, affecting groundwater recharge in water-scarce cities, such as Los Angeles, looking to harness local water resources. In the face of growing water demand, informing on opportunities to maximize potential groundwater recharge can help increase cities’ resilience. WRF–Hydro, a physics-based hydrological modeling system, capable of resolving atmospheric, land surface, and hydrological processes at city scale, is adapted to represent urban impervious surfaces. The modified model is used to assess the hydrological implications of historical urbanization. Pre- and post-urban scenarios are used to quantify the impacts of impervious surfaces on the local water budget. Our results show that urbanization in LA has vastly decreased the potential for groundwater recharge, with up to half of the water inflow being redirected from infiltration in highly urbanized watersheds, while doubling surface runoff’s share of the city’s water budget, from ~15% to 30%. This study not only sheds light on the role of imperviousness on groundwater recharge in water-scarce cities, but also offers a robust and transferable tool for the management of urban land and water resources.