Industrial wastewater discharge has become the main cause of water pollution in China. However, the spatial interaction mechanism between industrial structure and water pollution is still unclear. Accordingly, we evaluated and analyzed spatiotemporal changes of the agglomeration pattern of pollution-intensive industrial enterprises and the evolution of the water environmental pollution pattern, as well as the correlation between them. The study results show that the polluting industrial enterprises were located mainly along the Yangtze River and Taihu Lake Basin in southern Jiangsu in 2013 and 2018. However, we observed a spatial trend of pollution transfer to northern Jiangsu. The industrial water pollution discharge presents the distribution pattern of facing rivers, seas, lakes and cities. Papermaking and paper products industry are the leading factors of COD and NH3–N pollution, with explanatory power of 0.3666 and 0.6201 respectively. The spatial positive coupling effect between the concentration degree of polluting enterprises and the intensity of water environment pollution discharge is 94.95% of the region. The spatial agglomeration of polluting industrial enterprises is an important cause of water environment pollution. They promote and couple each other, proving the existence of “Pollution haven” and “Porter hypothesis".