Biogeochemical cycling of internal bioavailable organic phosphorus (OP) is an important source for algal bloom after exogenous P inputs are controlled. Biogeochemical cycling may be affected by hydrological processes and the water cycle and eventually result in water quality deterioration and accelerated lake eutrophication. Poyang Lake is the largest freshwater lake in China. The hydrological condition of the lake has significantly changed since 2003, thereby causing a continuous decline in water level. In this study, sediments were obtained from different elevations and different hydrological conditions in Poyang Lake. The sediments were subjected to sequential extraction and enzymatic hydrolysis to determine the transformation of OP into various chemical forms, their bioavailability, and the exchange between the sediments and overlying water. Results suggested that the descending water level caused by the changes in hydrological conditions was one of the major factors affecting OP dynamics. Long exposure of sediments resulted in high OP content and increased availability. The increased OP content in exposed sediments was primarily derived from H2O-Po and NaOH-EDTA-Po. Moreover, the increased OP availability in exposed sediments was mainly attributed to the increasing amount of orthophosphate caused by processes governing sediment exposure, promotion of OP release, and transformation of chemical forms from nonlabile to labile. Sediment exposure time and area have considerably expanded since 2003; hence, the amounts of OP and orthophosphate in the sediments have increased by as much as 600 and 120 tons in the lake every year, respectively. Although the increase in orthophosphate only accounted for 6% of the external total phosphorus, the local region may exhibit higher risk for OP release from the sediments, thereby accelerating quality deterioration. Therefore, maintaining reasonable hydrological conditions is important to protect Poyang Lake water.