The urban water sector significantly contributes to energy consumption and greenhouse gas (GHG) emissions. Detailed assessment of the wastewater system input provides opportunities for improving the water, energy, and emissions nexus. The inflow of water not requiring treatment into wastewater systems is acknowledged worldwide. These undue inflows can increase the footprint of these systems. Together with flooding and discharges, monitoring of undue inflows is not a common practice in water utilities. Three levels of analysis are proposed to assess the magnitude of the impact of undue inflows in the water–energy–greenhouse gas (W-E-G) emissions nexus: at a national level, calculation of performance indicators using yearly data; at the utility level, performance indicators calculations using yearly, monthly, and sub-daily data; at the subsystem level, calculations using mathematical modeling. Results show the implications of undue inflows on energy and GHG emissions, including the effect of flooding and discharges. The importance of undue inflows in the W-E-G nexus is sustained by the results of three case studies in Portugal. Each level of analysis is tailored to the information available, allowing a step-by-step understanding of the relationship between water, energy consumption, and emissions of the urban drainage inflows.