Polyphosphate (poly-P), a phosphorus component that is widely present in organisms and exhibits high biological activity, plays a critical role in the phosphorus biogeochemical cycling in eutrophic water bodies. To elucidate the degradation and transformation processes of poly-P at the sediment-water interface and within the water column, as well as its response to key environmental factors in lake sediments, in situ samples were collected from the Zhushan Bay area of Lake Taihu. These samples were used to simulate near-natural conditions for studying the degradation and transformation of poly-P. The results indicated that under near-natural conditions, the short-term hydrolysis rate of dissolved poly-P showed no obvious upper limit and increased with rising concentrations. After two days, the soluble reactive phosphorus (SRP) concentration generated by the hydrolysis of high-concentration poly-P could reach (0.1±0.01) mg/(L·d). The hydrolysis of poly-P was primarily driven by biological degradation, with key factors influencing the degradation rate including dissolved oxygen (DO), carbon sources, temperature, and sediment resuspension caused by disturbances. Low DO accelerated the hydrolysis of poly-P and brought the SRP to its peak 12 hours earlier. The addition of carbon sources slightly increased the hydrolysis rate and promoted sustained SRP release throughout the incubation period, with a net increase reaching twice that of the control group. Low temperatures significantly reduced the hydrolysis rate, although the overall SRP continued to rise. Disturbances that led to sediment resuspension increased both the hydrolysis rate of poly-P and the peak of SRP. In the sediment, poly-P mainly existed in a strongly bound form within the Al-P fraction, undergoing continuous release and further hydrolysis, while only trace amounts were present as free poly-P in the sediment and pore water. Dissolved poly-P could rapidly settle and hydrolyze within 48 hours under near-natural conditions, contributing to the sustained supply of SRP to the water column. This study on the occurrence and rapid hydrolytic turnover of poly-P in the water column provides insights into tracing and clarifying the sources of active phosphorus that fuel algal cell proliferation during the summer and autumn seasons. It also sheds light on the biogeochemical processes involving polyphosphate in the phosphorus cycle of water bodies.