To explore the impact of changes in physical, chemical and biological processes on hydrochemistry and carbon cycle caused by damming, we investigated the flux of suspended particulate and the spatiotemporal variations of major cations and anions (Ca²⁺, Mg²⁺, Na⁺, K⁺, HCO₃^-, SO₄^2-, Cl^-) in three karst reservoirs in Guizhou Province, i.e. Puding Reservoir, Pingzhai Reservoir, and Lake Hongfeng, for a whole hydrological year. The results showed that carbonate weathering and algae photosynthesis controlled the spatiotemporal variations of ion concentrations. The hydro-chemical type of Lake Hongfeng is Ca-Mg-HCO₃-SO₄, while it is Ca-HCO₃-SO₄ in Puding Reservoir and Pingzhai Reservoir. During the summer period, as the result of carbonate precipitation induced by algae photosynthesis, the concentrations of Ca²⁺, HCO₃^-, and SiO₂ in the surface water decreased by 20.87%-44.25%, 33.12%-51.18%, and 48.55%-96.34%, respectively. Our results also indicated that the stoichiometric relationships among C, N, Si could be affected by photosynthesis of aquatic photosynthetic organisms. Additionally, it is found that calcite precipitation regulated the Mg²⁺/Ca²⁺ in water column. Finally, the inorganic carbon fluxes in summer period calculated by sediment traps were 0.74 t/(km²·d), 1.36 t/(km²·d), 0.27 t/(km²·d) for Pingzhai Reservoir, Puding Reservoir and respectively, which are comparable with the fluxes estimated by the concentration differences in Ca²⁺ and HCO₃^- between surface and bottom water layers. The measured fluxes of inorganic carbon in Pingzhai Reservoir and Puding Reservoir by sediment traps are higher than the calculated one, suggesting a certain amount of allochthonous inorganic carbon input due to the strong hydrological condition. Therefore, it is an alternative way to estimate the deposition flux of inorganic carbon in karst reservoirs by using vertical variations in ion concentrations in stratification period.