Biological carbon pumps (BCPs) convert dissolved inorganic carbon (DIC) into autochthonous organic carbon (AOC), which is the key to form long-term stable carbonate weathering-related carbon sink. The DIC fertilization may increase the strength of BCP. As a phase of BCP, eutrophication is one of the major problems in surface water environments which shows poor water quality with harmful cyanobacteria blooms. It is generally believed that the controlling elements of eutrophication are nitrogen (N) and phosphorus (P), while the controlling elements of BCP also includes carbon (C). Meanwhile P removal by BCPs through the coprecipitation of P with calcite and Fe (III) oxyhydroxide colloids decreases its content in water bodies and prevent water from cyanobacteria eutrophication. In the present study, we examine the seasonal variations of general physiochemical parameters of the surface water, DIC, total N and total P concentrations, chlorophyll concentrations in three karst river-reservoir systems (PZR, PDR and HFR) in Guizhou Province, Southwest China. The phytoplankton community structure dynamics and the settling flux of the total P and P fractions in the settling particulate matter in PZR and HFR were also examined. It was found that: (1) the nutrient limitations of BCPs shifted from C-limitation to N- or Plimitation after the rivers were dammed; (2) P removal by BCPs reduced the total P concentration and increased the stoichiometric N:P ratio in surface waters; (3) P removal by BCPs alleviated the development of eutrophication by decreasing the relative abundance of Cyanobacteria. Our results demonstrate that the damming of a river may shift the nutrient limitation patterns of dammed karst rivers and the P removal by BCP may retard the development of water body into Cyanophyta-type eutrophication. This may have important implications for eutrophication control (i.e., strengthening BCP effect via DIC fertilization) in HCO3-Ca type surface water, especially in karst areas, which cover about 15% of the world land surface.