The water-energy-carbon nexus (WECN) has raised the attentions in the past years due to the shortages of water and energy resources, climate change and their close connection. It is critical to study WECN in water network systems due to their energy- and carbon-intensive characteristics. In optimization of WECN in water network planning, decision makers with conflictive objectives may have different decision-making power levels. In this study, an integrated Graph Theory-Based Bi-Level Water Network Planning Model, named GraBiL is developed, which represents a methodological contribution to the challenge of quantitative interrelationships of WECN and hierarchical decision-making problem in regional-scale water network planning. The GraBiL model has improved upon the existing bi-level programming and graph theory-based method for solving spatial layout optimization in two-level decision-making problem. Two-level conflictive objectives including minimizing total system cost and maximizing energy saving are considered. Fuzzy uncertainties associated with water loads are quantified. The impacts of carbon emission control on total system economic costs, energy consumption and the optimal water network planning are effectively addressed. The results from a hypothetical case study indicate that enhanced overall satisfaction for meeting the two-level objectives can be achieved with the proposed GraBiL model. Optimal water network planning schemes including spatial layout under four representative carbon emission control scenarios are compared. The proposed model has provided insight into quantitative interrelationships of WECN, hierarchical decision-making, optimization of water network spatial layout and quantification of fuzzy uncertainty associated with water loads in regional-scale water network planning.