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Stress from mixtures of synthetic chemicals is among the key issues that have significant adverse impacts on the marine ecosystems. A robust screening workflow integrating toxicological-based ranking schemes is still deficient for comprehensive investigation on the main constituents in chemical mixtures that contribute to the ecological risks. In this study, the presence and compositions of a collection of priority pollutants were monitored by suspect screening analysis of seawater and estuarine water samples from the semiclosed Bohai Sea. In total, 108 organic pollutants in nine use categories were identified. Pesticides, intermediates, plastic additives, and per-and polyfluoroalkyl substances were the extensively detected chemical groups. Varied distribution patterns of the pollutants were illustrated intuitively in distinctive sampling areas by hierarchical cluster analysis, which were mainly influenced by run-off inputs, ocean currents, and chemical use history. Ecological risks of chemicals with quantified residue levels were first assessed by the toxicity-weighted concentration ranking scheme, and pentachlorophenol was found as the main contributor in the investigating areas. By optimization of multiple alternative variables (e.g., instrumental response and detection frequency), extended ranking of all the identified pollutants was plausible under the toxicological priority index framework. Similarity in toxicological endpoints of the prioritized pollutants could further been screened by ToxAlerts. Aromatic amine was highlighted as the most frequently detected structural alert (SA) for genotoxic carcinogenicity and mutagenicity. These findings fully demonstrate rationality of the ranking schemes integrated into the suspect screening analysis for profiling contamination characteristics, assessing ecological risk potentials, and prioritizing SAs.