Urban areas provide strategic settings for attaining more sustainable urban systems. This paper provides fivefold contributions to the literature based on the Sustainable Development of Energy, Water and Environment Systems City Index. A comprehensive benchmarking of 120 cities is undertaken of which the first three cities are found to be Copenhagen, Stockholm, and Helsinki. Uncertainty and sensitivity analyses are conducted by comparing the original ranking with those based on Monte Carlo simulations and three aggregation schemes with and without the use of the geometric mean. The ranking of cities that take place in the 95% confidence interval and strong coefficients of correlation are found to suggest aspects of index robustness. As the third contribution, a scenario that represents the cross-sectoral strategy of utilizing residual energy in the urban vicinity from the industry, thermal power generation, wastewater, and urban biowaste is applied to 60 cities. The integration of data from the Pan-European Thermal Atlas provides additional practical value to local decision-makers who can assess possible improvements in city performance through such an approach. Fourth, 13 city pairs of 3 or more cities with the same above or below average performances across the dimensions of the index are identified as another means of supporting policy-learning opportunities. The fifth contribution synthesizes the original results of the research work to discuss the need for integrated urban transitions and proposes a vision for cities to envision the sustainable development of urban energy, water and environment systems. The research work provides analytical support to cities in a time when local actors are tasked with a mission that is nothing less than leading the transition to net-zero emissions by mid-century.