Large quantities of chemicals were discharged into the aquatic environment due to human activity and rapid development of economy, which may cause many adverse effects on the aquatic ecosystem and human health. Thus, a systematic approach is needed to prioritize pollutants for environmental monitoring purposes. A multi-criteria scoring method using 5 criteria, such as occurrence, persistence, bioaccumulation, ecotoxic risk, and human health risk, was developed to identify priority pollutants that require greater attention. The occurrence attribute was characterized using sub-attributes concentration and detection frequency based on the measured concentration in field environment. The persistence and bioaccumulation attributes were characterized by biodegradability and octanol-water partition coefficient, respectively. The ecotoxic risk attribute was characterized by risk quotients, which was calculated based on species sensitivity distribution and assessment factor. The human health risk attribute was characterized using sub-attributes incremental lifetime cancer risk and hazard indicator. A priority list of pollutants was developed for Zhangdu Lake using this multi-criteria scoring method, which included 11 polychlorinated biphenyls, 8 organochlorine pesticides, 6 polycyclic aromatic hydrocarbons, 4 volatile organic compounds, 4 phthalate esters and 8 metals. In addition, the generalized nature of the multi-criteria scoring method could be customized for specific geographical locations and establish site-specific priority list. The priority list will further serve as a basis for selecting candidate pollutants for future site-specific monitoring in surface water.