Excessive phosphorus (P) enrichment is the critical cause of eutrophication in the lake water. Organic P (P) mineralization processes induced by alkaline phosphatase (APase) regulated by phoD-encoding microorganisms in the lake ecosystems was still ambiguous due to the transseasonal shift of water temperatures and depths. Different P pools in the water and sediments of Shijiuhu Lake at varied seasons were measured using chemical extraction methods and solution P NMR. The alkaline phosphatase activity (APA) in the sediments were assessed together with enzyme kinetic parameters. The abundances and compositions of microbial communities encoding functional gene phoD were also obtained using high-throughput sequencing. The results showed that P concentrations remarkably increased from winter toward spring when having higher water depths due to the terrigenous input and biomass deposition. Noteworthy elevation in the PO- concentration was observed in the interstitial water during the spring, particularly at around 5 cm sediment depth with value reaching as high as 0.43 mg/L. The degradation and mineralization of momoesters and diesters with higher concentrations in the sediments of spring aggravated the PO- load in the interstitial water. Higher APA reaching 91.6 μg/(g·h) in spring was responsible for the mineralization of P. Remarkably upwards increasing of absolute abundance of phoD-encoding gene in spring reaching up to 2.6 times of that in winter facilitated the generation of APA in spring. Cobetia and Calothrix followed by Aquabacterium and Mitsuaria were the most abundant phoD-encoding genera with relative abundance > 4%. Weakly positive correlation between dominant bacterial genera and APA and P fractions suggested that low-abundance genera was also involved in the APA generation and P hydrolysis. These results indicate that spring with high water temperature and depth facilitate the mineralization of P in the sediment and increase of labile PO load in the water, further provide valuable information for the management of eutrophic lakes.