The seasonal fluctuation of phosphorus in shallow water lakes is a crucial process in the response of lake ecosystems to environmental changes. Unravelling the seasonal fluctuation pattern of phosphorus and its influencing factors in lakes is key to scientific and effective lake management. This study utilized 12 years of continuous monthly monitoring data from Lake Chaohu to analyze the seasonal variation pattern of phosphorus and its driving factors. The results indicated that phosphorus in Lake Chaohu exhibited a distinct intra-annual fluctuation pattern. The period from February to April represented the low values of phosphorus, which gradually increased thereafter, with the peak phosphorus concentration occurring from August to October, reaching the annual high. During the high phosphorus period, the total phosphorus concentration was 0.058 mg/L higher on average than the low phosphorus period, representing an average increase of 84%. Moreover, this fluctuation amplitude increased gradually from east to west. The intra-annual variation patterns of phytoplankton biomass and chlorophyll-a did not precisely align with the phosphorus fluctuation pattern. The peak values of phytoplankton biomass occurred earlier in the year than the peak phosphorus values, and there was a period of substantial phytoplankton distribution even in winter when phosphorus concentrations were relatively low. The explanatory power of algal intra-annual fluctuation amplitude on phosphorus fluctuation amplitude was less than 10%, indicating a limited influence of phytoplankton's intra-annual changes on the seasonal phosphorus fluctuation in Lake Chaohu. The intra-annual fluctuation pattern of phosphorus in Lake Chaohu was likely primarily driven by the natural release of internal phosphorus, with limited evidence of the regulatory effects of algal pump suction and external pollution entering the lake. This study enhanced our understanding of the seasonal variation of phosphorus in shallow lakes and held significant scientific implications for formulating strategies to control internal pollution in lakes.