Organophosphorus compounds (OPCs) pose potential hazards to human health and aquatic ecosystems. However, limited knowledge of emerging OPCs beyond organophosphate esters (OPEs) hinders a thorough understanding of the environmental occurrence and exposure risks. Through target, suspect, and nontarget screening analysis, 64 OPCs were successfully identified in Chinese estuarine waters, including 24 known OPEs and 40 emerging analogues (i.e., quaternary phosphonium, phosphine oxide, organophosphonate, and organothiophosphate esters). Domestic wastewater and agricultural and industrial discharges were factors influencing the OPC distribution patterns. In particular, quaternary phosphoniums and phosphine oxides accounted for over 50% of the total OPC loading in the Yellow and Jia Rivers, which were likely polluted by phosphorus-related industries. Risk quotient (RQ) calculations showed that tetrabutylphosphonium contributed the most to algae toxicity due to the biocidal effects of onium salts, while chloroalkyl OPEs dominated the ecological risks for daphnia and fish. The multicriteria decision analysis approach was further introduced for relative chemical ranking by considering the variations in hazard criteria of environmental occurrence, fate, and toxicity of the OPCs. The results indicate that aryl phosphoniums and aryl phosphine oxides have a hazard priority similar to that of the OPEs and, therefore, require more attention.