This study aims to evaluate the performance of groundwater-based tube well irrigation systems of Sarlahi District in Nepal considering a water–energy–food nexus approach. The deep tube well (DTW) irrigation systems showed better performance over shallow tube well (STW) irrigation systems in terms of water supply and agricultural output per unit of irrigated area. On the other hand, the STW-based irrigation systems showed better performance in terms of energy use, management operation and maintenance (MOM) cost and benefit–cost ratio compared to DTW-irrigated systems. The productivity of irrigation water and energy input to major crops showed the best performance for maize followed by rice and wheat. The simulated yields of cereal crops through the AquaCrop model showed significant scope for enhancing crop yields and associated benefits through judicious use of water and fertilizer.