The Pearl River (China) and its tributaries receive discharges of treated/untreated domestic sewage and industrial wastewater throughout the entire drainage basin. The river provides source water for many local inhabitants, and there is great concern over its pollution status. Fifteen sediment samples were collected from source water areas in the Pearl River Delta, and analyzed for the occurrence and distribution of 2 classes of emerging pollutants, organophosphorus flame retardants (OPs) and synthetic musks. In most sediments, 5 polycyclic musks and 2 nitro musks were detected, and galaxolide (1,3,4,6,7,8-hexahydro-4,6,6,7,8,8-hexamethylcyclopenta (g)-2-benzopyran [HHCB]) and tonalide (7-acetyl-1,1,3,4,4,6-hexamethyl-1,2,3,4-tetrahydronaphthalene [AHTN]) were the predominant components, with concentrations of 0.030 to 547 and 4.31 to 439 ng/g, respectively. Seven widely used OPs were found in most sediments, at varying total concentrations from 1.79 to 143 ng/g, with tris(2-butoxyethyl) phosphate (TBEOP), tris(2-chloro-isopropyl) phosphate (TCIPP), and triphenyl phosphate (TPHP) being the main components. The results indicated that industrial discharge and domestic sewage played important roles for synthetic musk and OP distribution in sediments in the study area. In general, higher levels of OPs and synthetic musks were found in Guangzhou, Foshan, and Dongguan, suggesting a significant impact from industrial discharges and the dense population of these regions. Environ Toxicol Chem 2018;37:975-982. © 2017 SETAC.