In order to research the changing process of the pollution from the formation of Nansihu Lake, this study determined the isotope age and depositional rate and analyzed the organic geo-chemical quotas and heavy metal quotas of two sedimentary profiles of Weishan and Dushan lakes. Research results showed that from the formation of Nansihu Lake, the change of the pollution could be divided into four phrases. At the early phrase of the formation, the organic matters of the lake mainly derived from the exotic matters and had a close relation to the effect on the water and sands from the Huanghe (Yellow) River. At the middle and late phrases of the development, the endogenous matters of the lake became the main and stable source of the organic matters. The overflow of the Huanghe River, the excavation of the Grand Canal and the cut of trees caused the changes of the historic pollution. In recent 20 years, the modern industrial pollution from the organic matters and heavy metals has an increasingly heavy tendency.