When water utilities establish water loss control programs, they traditionally focus on apparent loss rather than real loss when considering economic feasibility in the water sector. There is an urgent need for new management approaches that can address complex relationships and ensure the sustainability of natural resources among different sectors. This study suggests a novel approach for water utilities to manage water losses from the water-energy (WE) Nexus perspective. The Nexus model uses system dynamics to simulate twelve scenarios with the differing status of water loss and energy intensities. This analysis identifies real loss as one of the main causes of resource waste and an essential factor from the Nexus perspective. It also demonstrates that the energy intensity of each process in the urban water system has a significant impact on resource use and transfer. The consumption and movement of resources can be quantified in each process involved in the urban water system to distinguish central and vulnerable processes. This study suggests that the Nexus approach can strongly contribute to quantifying the use and movement of resources between water and energy sectors and the strategic formulation of sustainable and systematic water loss management strategies from the Nexus perspective.