In the past decade, organophosphate esters (OPEs) undergo rapid increase in production and use. Meanwhile, owing to their additive property, OPEs exhibit liability to escape from related products and therefore ubiquity in various environments. Moreover, numerous researches verify their bioavailability and negative effects on biota and human, hence their occurrence and associated risks have caught much concern, particularly those in aquatic systems. So far, however, OPEs in water are generally investigated as a whole, their phase distribution and behavior in waterbodies are incompletely characterized. We examined 25 OPEs in water (including dissolved and particulate phases), sediment, and sediment core samples from the Lian River, which flows through the Guiyu e-waste recycling zone and Shantou specific economic zone in South China. Compared to most global waterbodies, the Lian River showed high or ultrahigh OPE levels in both water and sediments, particularly in the reaches surrounded by e-waste recycling and plastic-related industries, which were the top two greatest OPE sources. Non-industrial and agriculture-related anthropogenic activities also contributed OPEs. Sediment core data suggested that OPEs have been present in waters in Guiyu since the 1960s and showed a temporal trend consistent with the local waste-recycling business. The phase distribution of OPEs in the Lian River was significantly correlated with their hydrophobicity and solubility. Owing to their wide range of physicochemical properties, OPE congeners showed significant percentage differences in the Lian River water and sediments. Generally, OPEs in water reflect their dynamic real-time inputs, while those in sediment signify their accumulative deposition, which is another cause of their phase distribution disparities in the Lian River. The physicochemical parameters of OPEs first imposed negative and then positive influences on their dissolved phase-sediment distribution, indicating the involvement of both the adsorption of dissolved OPEs and the deposition of particle-bound OPEs.