Following recent rapid industrialization, China is now one of the largest producers and consumers of organic chemicals in the world. This is compounded by variable regulatory oversight with respect to storage, use and waste management of these chemicals and their byproducts. This review synthesizes the data on the distribution of selected persistent organic pollutants (POPs) in waters in China. Surface water heavily polluted with POPs is distributed in the Yangtze River Estuary, Pearl River Delta, Minjiang River Estuary, Jiulongjiang Estuary, Daya Bay, Taihu Lake, and the waterways of Zhejiang Province, where concentrations of Polycyclic aromatic hydrocarbons (PAHs), organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) frequently exceed both international and Chinese guideline values. These areas are mainly distributed along the southeast coast of China, within or downstream of major manufacturing districts, intensive agricultural basins, and other industrial centers. A comparison of the levels of OCPs in the aquatic environment of China with other indicative regions worldwide shows comparable levels of pollution (overall range from below detection limit (BDL) to 5104.8 ng/L and regional means from 2.9-929.6 ng/L). PAHs and PCBs pollution appear to be particularly serious in China (PAHs overall ranging from BDL to 474,000 ng/L with regional means from 15.1-72,400 ng/L; PCBs from BDL to 3161 ng/L with regional means ranging from 0.2-985.2 ng/L). There is as yet limited evidence of serious perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA) pollution. We discuss major sources and processes responsible for high POP occurrence using a range of measures (including diagnostic ratios of different compounds), regulatory oversight and policy gaps in the control of POPs in China, and potential long-term health and ecological effects.