Abstract: The Lixia River hinterland is a typical aquaculture base in plain river network area. Lakes in this area are mostly developed for polders. Affected by complex water systems and slow flow, heavy metal is easy to be detained once it enters into the aquatic ecosystem, leading to a series of water environmental problems and food safety danger. Geoaccumulation index and Hakanson potential ecological risk index were used to evaluate heavy metal pollution in sediment phase of 28 typical lakes in the Lixia River hinterland. The sources of heavy metal pollution were analyzed partly qualitatively and partly quantitatively based on principal component analysis. Correlation analysis was conducted to find out the influences of industry discharge and polder aquaculture on heavy metals concentration. The results showed that the Hg, Zn and Cd in sedimentary phase were the major pollution elements with the concentrations 5.6, 1.9 and 1.4 times of the background values, respectively. The comprehensive potential ecological risk index of heavy metals ranged from 152.4 to 599.4. The source of Hg in sediment phase is different from the other 7 elements, perhaps affected by historical thermal power production. The closer the distance between lake and chemical plants, the higher concentration of Hg in sedimentary phase (r=0.42). Organic matter is easy to combine with Hg in sediments. The higher concentration of TOC, the higher concentration of Hg in sedimentary phase (r=0.54). The closer the lakes to the metal processing industry (such as alloy factory, electroplating factory), the higher concentration of Zn (r=0.68) and Cd (r=0.59) in sedimentary phase. Zn and Cd can easily accumulate in sediments due to the slow and uncontinuous water flow caused by the polder aquaculture. The above research conclusions can provide scientific basis for heavy metal pollution control and food safety protection in plain river network area.