Agricultural intensification is increasing global demand for water, with groundwater especially susceptible given its year-round reliability. Climate change impacts on groundwater recharge exacerbate uncertainties for future access and use, especially for large aquifers across alluvial plains such as the Indus Basin of Pakistan. To generate better understanding of climate change impacts on groundwater balances in such contexts, we used MODFLOW 2005 to quantify the groundwater budget of the Northern Rohri Canal Command Area under RCP 4.5 and 8.5 climatic scenarios, while also taking climatic regionalisation into account. Under a baseline scenario, total annual pumping in the northern Rohri command was estimated to be 3.619 billion cubic metres (BCM), and the total net loss in storage over the simulation period from October 2010 to April 2014 was estimated at 1.244 BCM per year. By 2047, net decline in storage is projected to more than double to 2.185 per year under RCP 4.5 scenario and 2.214 under RCP 8.5. Our estimates suggest that a sustainable yield across the command area should be managed at approximately 3 ± 0.3 BCM per year to ensure sufficient adaptive reserves of groundwater for access during times of drought and inadequate surface supply, while also reducing waterlogging impacts from high watertables. This first-time estimate of sustainable yield provides irrigation system managers with an overall guide from which divisional-scale measures to achieve the goal can be identified through stakeholder engagement.