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The phosphorus fate is critical to aquatic environment and ecosystem in lake. The relationship of phosphorus distribution in different mediums remains unknown under the fluctuation of phosphorus balance steady-state in lake. This study investigates the phosphorus balance of import and export in the Poyang Lake from 1990 to 2019, uncovering the transitional process of phosphorus balance steady-state and its influence on the phosphorus distribution relationship in different mediums. Our finding demonstrates that the phosphorus balance steady-state underwent four transitions during the study period of 1990–2019, resulting in a more fragile lake environment and ecosystem, with shorter intervals between quasi-balance states in Poyang Lake. The rate of sediment phosphorus burial and net phosphorus deposition increased significantly before the third phosphorus balance steady-state (2011–2013). However, the net deposition rate decreased by 5.3% with an increase in aquatic phosphorus after the third transition of phosphorus balance steady-state (2014) in Poyang Lake. Sediment played a significant role in redirecting from a net phosphorus sink to a net phosphorus source for water environment. The influence of phosphorus retention and sediment burial shifted from antagonism to synergism in increasing phosphorus content of waterbody, leading to a 5.4% rise in potential sources of aquatic phosphorus loading. These findings strengthen our understanding of phosphorus cycling and offer guidance for managing water environments in lakes. This work plays a vital role in regional water quality maintenance and water supply safety.