Agricultural production in arid and semi-arid regions is particularly vulnerable to climate change, which, combined with projected food requirements, makes the sustainable management of water resources critical to ensure national and global food security. Using South Africa as an example, we map the spatial distribution of water use by seventeen major crops under current and future climate scenarios, and assess their sustainability in terms of water resources, using the water debt repayment time indicator. We find high water debts, indicating unsustainable production, for potatoes, pulses, grapes, cotton, rice, and wheat due to irrigation in arid areas. Climate change scenarios suggest an intensification of such pressure on water resources, especially in regions already vulnerable, with a country-scale increase in irrigation demand of between 6.5% and 32% by 2090. Future land use planning and management should carefully consider the spatial distribution and local sustainability of crop water requirements to reduce water consumption in water risk hotspots and guarantee long-term food security.