Impacts of a range of climate change scenarios on the WEFN in the Indus Basin were modeled and then the potential of different alternative water allocation mechanisms and water infrastructure developments to address growing water, energy and food security concerns in the country were assessed. Results show growing water and energy use under hotter and wetter climate conditions. While more flexible surface water allocation policies can mitigate negative climate change impacts on agricultural water and energy use allowing for larger crop and hydropower production, such policies might also increase the inter-annual variability of resource use. Moreover, a more flexible surface water allocation policy would increase surface water use in the basin, while groundwater and energy use would be lower. Study results can inform the WEFN in areas with similar hydro-climatic environments, such as California and Central Asia. Further integration of a groundwater model and an energy market model and explicitly addressing changes in food and energy demand as a result of demographic dynamics are three areas for future study.