River Erguna is the Sino-Russian boundary river which has been widely concerned both by Russia and China due to the water quality and water resources management. As one class of persistent organic pollutants, no enough attention is paid to investigate the behavior characteristics and risk of organochlorine pesticides (OCPs) in the rivers originated from forests and grasslands distributing in the middle-high latitude belts. This work investigated the source and characteristics of OCPs and evaluated their health risk assessment in the water system of River Erguna for the first time. The concentrations of OCPs were ranged from not detected (N.D) to 5.4 ng L⁻¹ with the average of 2.2 ng L⁻¹. Source analysis indicated a recent DDTs (dichlorodiphenyltrichloroethane) input from the application in agricultural and forestry ecosystem in the drainage basin, whereas HCHs (hexachlorocyclohexanes) mainly originated from long-distance transmission or degradation of technical HCHs. Both the non-carcinogenic and carcinogenic risks were in the acceptable range, which is safe for the residents living along the Sino-Russian boundary river. This work would provide basic data set for the water quality and water sources management to avoid environmental dispute between Russia and China.