Dissolved organic matter (DOM) plays a vital role in the biogeochemistry of aquatic ecosystems. However, the mechanisms of DOM cycling in the water column during different seasons have not been fully elucidated to date. The differences in DOM degradation in summer, autumn, and winter water columns were evaluated in this study. The results showed that bacteria played an essential role in the degradation of DOM in the summer water column. Photochemical degradation was the primary degradation pathway of DOM in the autumn and winter water columns. Notably, while DOM is degraded, photosynthetic bacteria produce organic matter through photosynthesis to replenish the water column. EEM-PARAFAC analysis indicated more tryptophan component C1 in summer, but the contents of humic substance component C2 and terrestrial substance C3 were higher in autumn and winter. In summer, more tryptophan-like components were consumed by bacteria, and Cyanobacteria produced more organic matter through photosynthesis to replenish the water column. Moreover, a similar bacterial community structure and a more active tryptophan biosynthesis pathway were found in autumn and winter. Random forest models identified representative bacteria involved in the DOM transformation process in different seasons. The above findings may be helpful to explore the degradation characteristics of DOM in different seasons and predict the fate of DOM in the water column in the future.