The widespread construction of dams has created reservoirs that are significant sources of greenhouse gases, primarily driven by microbial processing of dissolved organic matter (DOM), yet the synergistic changes and interactions between microbial communities and DOM composition under dam operation remain poorly understood. This study investigated the spatial co-variation of prokaryotic communities and DOM along the hydrological gradient of the Three Gorges Reservoir (TGR). The results showed that the dam created distinct environmental gradients, leading to increased microbial α-diversity and a shifted community structure (e.g., enriched
Nitrososphaeria) near the Three Gorges Dam. Concurrently, DOM showed decreased humification index (HIX) and increased biological index (BIX), indicating a shift from terrestrial to microbially processed DOM. Network analysis demonstrated strong correlations between microbial taxa (e.g.,
Actinobacteria, Proteobacteria) and DOM components, revealing microbial involvement in DOM transformation. These findings demonstrate a dam-induced co-variation wherein hydrologically driven microbial assemblages degrade terrestrial humic substances, reducing aromaticity and influencing reservoir carbon cycling, which must be considered for assessing the climatic impact of hydropower.