The status of water resources in many coastal cities has become increasingly fragile. In a changing climate, the amount and intensity of rainfall have continued to decline, causing some coastal regions to experience severe drought and deteriorated water supply situation. This article presents a comprehensive study of the urban water metabolism of Cape Town, South Africa. A water mass balance framework was utilized to examine the city's water system across four distinct periods. In addition, the water-energy nexus before and after the drought crisis was evaluated. The key findings include a large amount of surface runoff in the Cape Town area that was not utilized before the drought crisis, resulting in a natural loss potential of water supply that is 2.54 times greater than water used for supply systems. During the drought, per capita water consumption dropped by a substantial 25%; at the same time, the total rate of water loss experienced a substantial decrease of approximately 21%. Since the pandemic, Cape Town's water resources policy has shifted to diversifying water sources, and the use of wastewater and natural water losses will be optimized by more than 32% in 2040 to achieve a water-sensitive city. Future research should explore the temporal and spatial dynamics of urban water flows, the impact of socioeconomic factors, and the integration of water system optimization models for enhanced urban water management.