Global climate change and intensive anthropogenic activities are affecting the variety and contents of dissolved organic carbons (DOC) in the aquatic systems. The potential response of planktonic bacteria to the changing carbon sources could influence the characteristics of carbon cycling in local waterbodies and even regional areas. In this study, eleven small and medium reservoirs were selected to quantificationally analyze the utilization of exogenous and endogenous organic carbon during the bacterial production and respiration using the stable carbon isotope analysis and a two-source mixing model. The eleven reservoirs were subsequently classified into exogenous (exogenous DOC/DOC>50%) and endogenous (endogenous DOC/DOC>50%) reservoirs according to the ratio of the two kinds of DOC sources. Results indicated that the concentrations of DOC and chlorophyll-a (Chl.a) and trophic level index were significantly higher in the endogenous reservoirs than in the exogenous reservoirs. It was observed that the bacterial metabolic rates of endogenous DOC could be significantly elevated with increasing primary productivity in the reservoirs. Specifically, the metabolic rates of endogenous DOC were improved for bacterial production in the endogenous reservoirs and bacterial respiration in the exogenous reservoirs, respectively. Moreover, the overall bacterial metabolic rates of DOC were promoted in the exogenous reservoirs with increasing primary productivity. In addition, a significant relationship was observed between dissolved inorganic nitrogen/phosphorus and bacterial respiration, indicating that the bacterial respiration could be suppressed with increasing nutrition concentration in the endogenous reservoirs but be strengthened with increasing nutrition concentration in the exogenous reservoirs. These results suggested that the release flux of greenhouse gas can be increased owing to the improvement of bacterial respiration with the elevating eutrophication levels in the exogenous reservoirs.