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We investigated residual levels of organochlorine pesticides (OCPs) and polycyclic aromatic hydrocarbons (PAHs) in water, soil and sediments from the Kaidu River catchment in Xinjiang, an arid zone in northwest China. Sediments from areas with highly polluted soil have higher OCPs and PAHs, caused by intensive anthropogenic activities. Pollution concentrations, however, were lower than those in Lake Bositeng indicating that the lake is a sink for pollutants in this region. Source analysis indicated that hexachlorocyclohexanes (HCHs) and dichlorodiphenyltrichloroethanes (DDTs) originated mainly from historical agricultural applications. DDTs in sediments of the Lake Bositeng Estuary, however, may contribute to pollutant resuspension, resulting from sediment disturbance, and recent inputs. Low-molecular-weight PAHs were predominant, indicating that PAHs originated primarily from low-temperature combustion processes and petroleum-derived sources. A risk assessment of OCPs and PAHs in soil and sediment, suggested that concentrations were not high enough to cause adverse biological effects in the aquatic ecosystem.