Discovering the inherent mechanisms between water cycle process and carbon emissions in urban water system is of important theoretical and practical significance for promoting water-energy conservation and low-carbon optimization. From the perspective of "water-energy-carbon" nexus, a theoretical framework and a series of calculation methods of carbon emissions within urban water system were established in this study. Based on statistical data from 2008 to 2017 and data obtained through questionnaires, the carbon emissions of water system in Zhengzhou city were calculated according to the energy consumptions of each subsystem. The characteristics of water-energy-carbon nexus in water system were demonstrated, based on which further analysis was made under different scenarios of carbon emission reduction potential. The main conclusions are as follows: (1) Water system of Zhengzhou city involves various subsystems, including water intake, water supply, water use, and wastewater treatment. The carbon emissions of urban water system were not only influenced by the amount of water supply and use, but also affected by the mode and distance of water delivery, energy type, structure and efficiency of operation facilities, and terminal use in each subsystem. Water use subsystem was the main source of carbon emissions, indicating that the main reason for the growth of carbon emissions was the increasing water demands driven by urban expansion and population growth. (2) There exist huge differences in carbon emission composition and intensity, as well as the temporal changing trends of carbon emissions among different water subsystems in Zhengzhou. Specifically, the intensity of energy consumption and carbon emissions of water intake and water use increased obviously, while it was relatively stable in water supply and wastewater treatment. Attentions should be paid to the increase of energy consumption of water intake and water use system, especially the increase of carbon emissions caused by long distance water supply and the reuse of raw sewage. (3) The different characteristics of "water-energy-carbon" nexus of different subsystems of water system in Zhengzhou were mainly affected by changes of water use, water treatment methods and processes, residential water use habits, water conservation awareness, natural conditions, and climate change. (4) In the future, water system efficiency should be improved to reduce energy consumption and carbon emissions. Effective measures include urban industrial and domestic water saving, water treatment process improvement, water saving promotion, water system optimization, low-carbon management, and energy efficiency improvement.