Water supply challenges in emergency situations have increased in recent years and there is a need for analyses targeting economic and environmental sustainability. Our study investigated the end-user water demand, the capital and operational costs, the carbon footprint, the freshwater availability and the risks surrounding water quality for several groundwater supply alternatives in Ugandan refugee settlements. We compared hand pumps, motorised pumps (solar, diesel and hybrid) and water trucking. The end-users’ survey highlighted the significant variability of water access. The economic evaluation showed that the breakeven year for solar and diesel pumps was greatly affected by the length of the water distribution systems (e.g., pipes, storage tanks), the chosen timeframe and the daily working hours of the diesel engine. When excluding capital investment, most alternatives were economically viable at the existing water fee (0.8 USD/m3), and solar driven pumps were down to 0.09 USD/m3. Finally, the combustion of diesel caused the highest CO2-eq emissions per m3. Water trucking is the worst option in both the economic and environmental analysis at 7–8 USD/m3 and >1 kg CO2-eq/m3. The methodology and the results of this paper will support decision-makers to build and finance sustainable water provision solutions in refugee settlements.