Lake Taihu is a large eutrophication lake, the endogenous pollution and release characteristics of sediments in different lake areas were significantly different. The study investigated and analyzed the variation of endogenous pollution and nitrogen and phosphorus diffusion fluxes in Xuhu (grass-dominated zone) and Zhushan Bay(algae-dominated zone) with different water depths. The results showed that: The total nitrogen content in the sediments of Xuhu Lake and Zhushan Lake was 2.59~3.33g·kg-1 and 2.95~3.63g·kg-1, and the total phosphorus content was 0.462~0.652g·kg-1 and 0.749~0.916g·kg-1, respectively. The nutrient content in the sediments of the algae lake area was significantly higher than that in the grass lake area, and the content fluctuated irregularly with the change of water depth. Phosphorus speciation analysis of sediments showed that: Ca-P were the main sediments in Xuhu Bay, and the proportion of Ca-P in total phosphorus decreased significantly with the increase of water depth.The phosphorus morphology in the sediments of Zhushan Lake was dominated by Fe-P, and the proportions of Fe-P, Al-P and Ca-P in the total phosphorus gradually increased with the increase of water depth. The SRP content at the sediment-water interface in the shallow water area of Xuhu is significantly higher than that in the deep water area, while the difference in Fe2+ and NH4+ concentrations between different water depths is relatively small. The SRP, Fe2+ and NH4+ contents at the sediment-water interface in the shallow water area of Zhu Mountain Lake are all higher than those in the deep water area.The endogenous release risk of Xuhu and Zhushan Lake was small, and the NH4+ diffusion flux of Xuhu Lake decreased first and then increased with the increase of water depth, and the NH4+ diffusion flux of Zhushan Lake increased significantly with the increase of water depth. The results play an important role in understanding the nitrogen and phosphorus migration of water depth at the sediment-water interface in the grass/algae lake area of Taihu Lake.