In recent years, the global carbon cycle has garnered significant research attention. However, details of the intricate relationship between planktonic bacteria, hydrochemistry, and dissolved organic matter (DOM) in inland waters remain unclear, especially their effects on lake carbon sequestration. In this study, we analyzed 16S rRNA, chromophoric dissolved organic matter (CDOM), and inorganic nutrients in Erhai Lake, Yunnan Province, China. The results revealed that allochthonous DOM (C3) significantly regulated the microbial community, and that autochthonous DOM, generated via microbial mineralization (C2), was not preferred as a food source by lake bacteria, and neither was allochthonous DOM after microbial mineralization (C4). Specifically, the correlation between the fluorescence index and functional genes (FAPRPTAX) showed that the degree of utilization of DOM was a critical factor in regulating planktonic bacteria associated with the carbon cycle. Further examination of the correlation between environmental factors and planktonic bacteria revealed that Ca²⁺ had a regulatory influence on the community structure of planktonic bacteria, particularly those linked to the carbon cycle. Consequently, the utilization strategy of DOM by planktonic bacteria was also determined by elevated Ca²⁺ levels. This in turn influenced the development of specific recalcitrant autochthonous DOM within the high Ca²⁺ environment of Erhai Lake. These findings are significant for the exploration of the stability of DOM within karst aquatic ecosystems, offering a new perspective for the investigation of terrestrial carbon sinks.