Understanding the water-energy-greenhouse gas (WEG) nexus in urban water systems (UWSs) is critical for sustainable development. However, this nexus is not studied comprehensively in developing countries. The UWS in developing countries generally follow conventional water treatment. There is partial wastewater collection and majority of wastewater is treated in septic tanks. This study analyses the total embodied energy and greenhouse gas (GHG) emissions from a typical Indian UWS. This study also analyses the changes in total embodied energy and GHG emissions when complete wastewater is treated in wastewater treatment plants. Process-based life cycle assessment approach is adopted incorporating construction and operation phase in the system boundary. The results show that the operational energy and piping infrastructure dominate total embodied energy use in the UWS. The total GHG emissions from the UWS were majorly contributed by operational energy with 60% share, followed by the septic tanks with ∼29% share. Complete wastewater collection and treatment would increase the total embodied energy by ∼21% and would decrease the GHG emissions by ∼11%. The methodological framework and data inventory presented in this study can be used to identify the hotspots of energy and GHG emissions in the UWSs, facilitating informed decision-making for its sustainable operation.