Carbonate mineral weathering coupled with aquatic photosynthesis on the continents is an important part of the global carbon cycle. The biological carbon pump is a key mechanism for stabilizing carbonate weathering-related carbon sinks. Little research has been done on the changes and control factors of biological carbon pump effects and their effects on hydrochemistry after the damming of river. In this study, two dammed karst rivers (Pingzhai Reservoir and Lake Hongfeng) were systematically sampled to study the changes and control factors of biological carbon pump effect and their effects on the variations of hydrochemistry. The results show that the hydrochemistry of the rivers have no obvious changes, while the hydrochemistry of the two reservoirs show significant seasonal variations. The temperature and pH of the two reservoirs are both higher in summer and lower in winter, while electrical conductivity (EC), HCO₃^- concentration and pCO₂ show lower in summer and higher in winter. The biological carbon pump effect which is indicated by the chlorophyll-a (Chl.a) concentration and dissolved oxygen saturation is stronger in summer and weaker in winter. Dissolved inorganic carbon is consumed by aquatic phototrophs to form organic matter and release oxygen, which are the main factors that cause the increase of pH and dissolved oxygen (DO) in summer, and the decrease of electric conductivity (EC), HCO₃^- concentration, and pCO₂ in winter. In the space, the Chl.a and DO concentrations of the reservoirs are larger than that in the rivers, and EC, HCO₃^- concentration and pCO₂ are lower than that in the rivers. This indicates the biological carbon pump effect of the reservoir is significantly increased due to river impoundment after the rivers were dammed. Correlation analysis of Chl.a with carbon, nitrogen, phosphorus concentrations and stoichiometry revealed that the biological carbon pump effect of the Pingzhai Reservoir and Lake Hongfeng is affected by carbon fertilization effect. The carbon fertilization effect of biological carbon pump detected here may indicate that aquatic photosynthesis in karst damped rivers may be controlled not only by N and/or P but also by C. This research may have implications for control of eutrophication in karst lakes with high alkaline.