To investigate the concentrations, spatial distribution, potential sources and mass fluxes of organochlorine pesticides (OCPs) and polycyclic aromatic hydrocarbons (PAHs) in waters from the Danshui River Basin, a total of 20 water samples were collected and analyzed from a karstic river in Western Hubei of Central China. The average concentrations of total OCPs and PAHs in the river water were 4719 pg·L−1 and 26.2 ng·L−1, respectively. The characteristic ratios of different isomers and the composition analysis of individual OCPs and PAHs revealed that HCHs originated from a mixed input of technical HCHs and Lindane, DDTs were mainly from technical DDTs, and PAHs mainly originated from biomass and coal combustion. The mass flux analysis showed that PAHs had a higher emission and heavier burden than OCPs in the Danshui River Basin. OCPs and PAHs emitted from agricultural or other human activities could enter the groundwater and then be transported to the surface/river water in the karst area. The adsorption of OCPs and PAHs by particles and the sedimentation of particles could be the primary processes to intercept these pollutants in the water of the karstic river system.