In this research, an interval two-stage stochastic fuzzy-interval credibility constraint programming (ISFICP) method was developed for water resources allocation among multiple water users under complexities and uncertainties. The method could reflect the multiple complexities of water resources management, also trade-offs between the system benefits and violation risks. Dongjiang River (DJR) Basin, which supplies water to several core cities in south China such as Guangzhou, Shenzhen, and Hong Kong, was applied as the real demonstrative case. The water resources system of DJR Basin is particularly complex due to it is the primary source water for Guangdong-Hong Kong-Macao Greater Bay Area (GBA). Through considering multiple complexities and uncertainties of the water resources system, such as natural, economic, and social conditions, ISFICP was developed to obtain potential water-allocation schemes. Probabilistic distribution, fuzzy-interval sets (FIS), and discrete intervals were introduced to represent the multiple uncertainties associated with the multiple complexities. The results indicated that the model could provide practical schemes for local decision-makers under multiple scenarios such as flow levels, credibility levels, and recycling rates.