Environmental water quality problems resulting from pollutant discharges have received extensive attention with the increasingly severe challenges facing global resources and the environment. A consideration of hierarchy within water resources-environment system (WRES) management under uncertainty can effectively improve the accuracy and applicability of management decisions. This study developed an interval fuzzy-credibility constrained two-level programming (IFCTP) model for WRES planning which considers uncertain information through the use of interval values and fuzzy sets and can also resolve conflicting goals among decision-makers in different departments. The IFCTP-WRES model was then formulated and applied for planning of the middle route of South-to-North Water Diversion Project (SNWDP) in Henan Province, China. Multiple water allocation, pollution control, and economic benefit solutions encompassing three departments and thirteen water-receiving cities involving dual uncertainties and varied credibility levels were examined. The results showed that: (1) the proportion of water resources allocated to ecological flows should increase from [14.12, 14.15]% to [17.97, 17.99]% over the entire planning period; (2) the proportion of water resources allocated to small cities (e.g., Huaxian County) should show a constant increase; (3) municipal wastewater can contribute more than half of the total pollutant load; (4) as compared to the economic benefit that can be obtained through solutions identified by two single-objective models, the interval fuzzy-credibility constrained programming environmental management system (IFCP-EMS) model and interval fuzzy-credibility constrained programming water resources management system (IFCP-WMS) model, that by the IFCTP-WRES model has higher by 5.0% and lower by 4.5%, respectively. These findings can provide abundant alternatives for achieving sustainable development and can help decision-makers to effectively plan WRES management under uncertainty.