Current-use pesticides (CUPs) are widely applied in agriculture; however, little is known about their environmental behaviors, especially in the freshwater–seawater transitional zone. Water and sediment samples were collected in an intensively human impacted river (Xiaoqing River) from the headwaters to Laizhou Bay to investigate the distributions and environmental fates of four CUPs: trifluralin, chlorothalonil, chlorpyrifos, and dicofol. These CUPs were frequently detected in water and sediment samples. ∑CUPs in water and sediment samples ranged from 1.20 to 100.2 ng L−1 and 6.6–2972.5 ng g−1 dry weight (dw), respectively. Chlorpyrifos and chlorothalonil were the most abundant CUPs in water and sediment samples, respectively. Spatial distribution of CUPs in the Xiaoqing River aquatic ecosystem was mainly influenced by point sources, agricultural activities, the dilution effect by seawater, and environmental parameters. Field-based sediment water partitioning coefficients, normalized by organic carbon (log Koc), were calculated. Interestingly, temperature and salinity exhibited significant impacts on the distribution of log Koc of the four CUPs. The effect of temperature on the distribution of log Koc of the four CUPs varied between the CUPs. In most water samples, the levels of chlorpyrifos exceed the freshwater screening benchmarks. Hence, urgent control measures need to be devised and implemented. Display omitted •Four CUPs were firstly reported in the surface waters and sediments from a river-estuarine system.•Chlorpyrifos in water and chlorothalonil in sediment were the most abundant CUPs, respectively.•Field-based distribution coefficients (Kd and Koc) were estimated for the four CUPs.•Temperature and salinity were main factors influencing the CUP distribution coefficients. CUPs were ubiquitous detected in the river-estuary systems and temperature and salinity were main factors influencing their distribution coefficients.