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Water production, utilization and recycle in urban system associated with a large amount of energy consumption and carbon emission that has increasingly international attention under sustainable development goals. In this study, a comprehensive urban water resources system management model is proposed under water-energy-carbon nexus and multiple uncertainties. The water-energy-carbon nexus was reflected in the processes of water extraction, water production and sewage treatment, and two objectives of maximizing the system benefit and minimizing carbon emission is transformed into two linear programming problem through the dual-objective interval fractional programming. Considering the interaction among water supply/demand, pollutants discharge control, energy consumption and self-energy utilization, indirect carbon emission as the main constraints, the developed model is applied to a typical water and energy sources shortage area of Qingdao city in north China. Multiple scenarios related to energy consumption and carbon emission control are designed to search the relationship among energy consumption, carbon emission and water resources allocation schemes. The results indicated that water demand as the main driving factor of energy consumption and carbon emission in urban water system cannot be directly limited through water supply structure adjustment. Through introducing self-energy supply (sludge utilization) and energy consumption control, water resources allocation schemes and water supply structure would be changed to improve energy saving potential with an obvious decrease trend of carbon emission intensity from 0.7921 tCO 2 /MWh to 0.5544 tCO 2 /MWh. The model could effectively provide reasonable urban water system management strategies under different water allocation demands and carbon emission challenges scenarios and deal with multiple uncertainties in decision-making process. [Display omitted] • Urban water resources system brings ecological environment issues. • A comprehensive urban water resources system management model is proposed. • Maximizing the economic benefits of per carbon emission to obtain the scheme. • Sludge utilization and energy consumption control can reduce carbon emission. • The model provides experiences for water-scarce regions around the world. [ABSTRACT FROM AUTHOR]