Discrepancies between water demand and supply are intensifying and creating a need for sustainable water resource process management associated with rapid economic development, population growth, and urban expansion. In this study, a scenario-based interval fuzzy-credibility constrained programming (SIFCP) method is developed for planning a water resource management system (WRMS) that can handle uncertain information by using interval values, fuzzy sets, and scenario analysis. The SIFCP-WRMS model is then applied to plan the middle route of the South-to-North Water Diversion Project (SNWDP) in Henan Province, China. Solutions of different water distribution proportion scenarios and varied credibility levels are considered. Results reveal that different water-distribution proportion scenarios and uncertainties used in the SIFCP-WRMS model can lead to changed water allocations, sewage discharges, chemical oxygen demand (COD) emissions, and system benefits. Results also indicate that the variation of scenarios (i.e., from S2 to S3) can result in a change of 9% over the planning horizon for water allocation in the industrial sector. Findings can help decision-makers resolve conflicts among economic objective, water resource demand, and sewage discharge, as well as COD emissions.