Dam construction significantly impacts river hydrodynamics, subsequently influencing carbon biogeochemical processes. However, the influence of hydrodynamic conditions on the migration and transformation of Dissolved Inorganic Carbon (DIC) remains uncertain. To bridge this knowledge gap, we integrated hydrochemistry, isotopic composition (δ13CDIC), and a hydrodynamic model (CE-QUAL-W2) to examine the distinctions, control mechanisms, and environmental effects of DIC biogeochemical processes in a typical large and deep reservoir (Hongjiadu Reservoir) under different hydrodynamic conditions. We evaluated hydrodynamic alterations through the Schmidt stability index and relative water column stability. The analysis disclosed that during weak hydrodynamics periods, the energy necessary for complete mixing the surface and deep water was 34 times higher (3615.32 J/m2 vs.106.86 J/m2), and stability was 13 times greater (312.96 vs. 24.69) compared to periods of strong hydrodynamics. Additionally, the spatiotemporal heterogeneity of DIC concentrations (1.4 % to -9.1 %) and δ13CDIC (-1.7 % to -19.5 %) from the dry to wet seasons reflected disparities in DIC control mechanisms under varied hydrodynamic conditions. Based on model simulations, our calculations indicate that during weak hydrodynamics periods, the enhancement of the biological carbon pump effect resulted in substantial sequestration of DIC, reaching up to 379.6 t-DIC·d−1 in the water. Conversely, during strong hydrodynamics periods, DIC retention capacity decreased by 69.2 t·d−1, resulting in reservoir CO2 emissions of 22.7 × 104 t, which were more than 7 times higher than during weak hydrodynamics periods (3.2 × 104 t). Our findings emphasize the discernible impact of hydrodynamic conditions on reservoir biogeochemical processes related to DIC. Considering the increasing construction of reservoirs globally, understanding and controlling hydrodynamic conditions are crucial for mitigating CO2 emissions and optimizing reservoir management.