Sedimentary phosphorus is a crucially potential source of phosphorus in the eutrophic lake ecosystem. Different ecological types are supposed to affect the presence and variation of sediment phosphorus. On the basis of field investigations, the total sediment phosphorus load in Zhushan Bay was 1,457.48 mg/kg, nearly four times that of the hydrophyte-dominated area. Thereinto, 41.1% was in the form of iron and aluminum-bound phosphorus, which explicitly indicated the phosphorus contamination there. Analytical methods such as Pearson correlation, contamination assessment and principle component analysis were conducted to find out that ācontaminationā was not equivalent to ārelease riskā. The contamination classification of East Lake Taihu was ācleanā in general. However, 63.3% of the total phosphorus could be mobilized under certain conditions. Therefore, light phosphorus loading does not equal to less release risk. In the long run, the implicit phosphorus release by the activation of organic phosphorus in hydrophytic areas needs close attention. This study provides a reference to understand the influence of hydrophytes and algae on the phosphorus cycle of sediment.