Urban water utilities are significant energy users and also key actors in decarbonisation. However, the integrated perspective of urban water supply and wastewater system emissions, the relevant driving forces, and the boundaries of inclusions or exclusions, are rarely discussed. This is due to widely disaggregated data, and complex issues regarding the boundary of the system being investigated. This work develops an innovative assessment approach to assess system-wide emissions. We investigate historical emissions from eight cities (representing 56 million people). This study answers the question: what are the emission trajectories of urban water supply and wastewater systems and influencing factors and the influence of system boundary inclusions? The results indicate that, in many systems, "additional" or "new" water sources such as desalination or long-distance water transfers can dominate the emissions trends. Inconsistent inclusion of infrastructure for these supplies complicates city comparisons. Additionally, clarity is needed on whether emissions from recycled water (potable and non-potable) is reported as water supply or wastewater emissions. The creation of water/wastewater-emission trajectories better illustrates trade-offs occurring with management - for example, water supply in Perth and Beijing. The trajectory also illustrates reductions achieved for 15 years, for example, water supply in San Diego (reducing 77 %) and wastewater in New York City, San Diego, Los Angeles and Tokyo (reducing 38, 44, 47, and 17 % respectively). Our integrated analysis method provides a new emphasis for more holistic management of the water cycle. By revealing system boundary issues in reporting and systematically assessing full water cycle emissions, we demonstrate how essential this is to enable comparison across complex systems and city and utility reporting schemes.