Abstract: To investigate the effects of exogenous functional microorganisms on microbial community structure, carbon metabolism characteristics, and organic carbon content in aquaculture water, we designed a blank control group, a feed control group, and three bacterial supplementation groups treated with Bacillus licheniformis, Lactobacillus plantarum, and Rhodopseudomonas palustris, respectively. We measured the total organic carbon (TOC), dissolved organic carbon (DOC), total bacterial count, microbial community structure, and carbon metabolism function to analyze their dynamic changes. The results showed that the addition of three beneficial bacteria significantly enhanced microbial metabolic activity and community diversity. On Day 7, the Shannon index in the bacterial supplementation groups reached 3.17–3.18, which was significantly higher than that in the control groups (p<0.05). The exogenous probiotics exerted limited influence on overall bacterial abundance and community succession. In the later stages, Pseudomonadaceae and Rhodobacteraceae became the dominant families. The degradation rates of TOC and DOC in the bacterial supplementation groups reached 59.0%–59.5% and 57.1%–57.7%, respectively, which were significantly higher than those in the blank control group (p<0.05). Among the three strains, R. palustris exhibited the strongest carbon source utilization capacity, B. licheniformis showed a clear advantage in degrading complex organic carbon, and L. plantarum exerted a mild and stable effect. This study indicates that the addition of Bacillus, photosynthetic bacteria, and lactic acid bacteria to aquaculture water can improve microbial community diversity and metabolic activity and accelerate organic carbon degradation.