Research on the environmental occurrence and behavior of organophosphate esters (OPEs) is very imperative. In this study, 12 targeted OPEs in the water and sediment samples collected from the middle and lower streams of the Yellow River (YR) and its tributaries during the dry, normal, and wet season were analyzed, to reveal their concentration, spatiotemporal variations, and ecological risks. The results indicated that the total concentration of OPEs (ΣOPE) ranged from 97.66 to 2433.30 ng/L in water, and from 47.33 to 234.08 ng/g in sediment. Tris(2-chloroethyl) phosphate (TCEP), tris(2-chloroisopropyl)phosphate (TCIPP), and triethyl phosphate (TEP) were the most abundant OPEs in the surface water and sediment. The OPEs levels in river water were ranked as the order of dry > normal > wet season. The ΣOPE concentrations in water and sediment were relatively high in the central and lower sections of the YR. The resorcinol-bis(diphenyl)phosphate (RDP) effectively transferred from the overlying water to the sediment. TCEP and RDP posed relatively higher ecological risk than other OPEs. Municipal and chemical industrial discharge might be sources of OPEs in the middle and lower streams of the YR.