The infiltration of organic-rich surface waters towards groundwaters, is known to play a significant role in carbonate weathering and in contributing to the atmospheric continental carbon sink. This paper investigated biogeochemical interactions in karst critical zones, with strong surface water /groundwater interactions, and in particular the role of planktonic microorganisms and riverine bivalves through the analysis of particulate organic matter (OM) oxidation on carbonate weathering. In the large Val d'Orléans fluviokarst aquifer (France), a 20-year monthly dataset of Nitrates, Dissolved Oxygen (DO), dissolved inorganic and organic Carbon (DIC and DOC) fluxes was gathered. The surface water-groundwater comparison of geochemical trends showed that planktonic microorganisms had drastically decreased in surface waters, related to the proliferation of Corbicula bivalves spreading and a decrease in nutrients. This decrease in planktonic microorganisms was followed by a DO increase and an DIC decrease at the karst resurgence. The degradation of planktonic microorganisms consumes DO and produces NO3, dissolved inorganic carbon (DIC) and a proton that in turn, dissolves calcite and produces DIC. Without the input from planktonic microorganisms, the fluviokarst has lost 29 % of this nitrification and 12 % of the carbonate dissolution capacities. Thus, the oxidation of particulate organic matter of planktonic microorganisms, which is part of heterotrophic respiration, appears to be a significant source of the inorganic carbon flux in riverine ecosystems. This shows how weathering can remain active under waters saturated versus calcite and suggests that the oxidation of organic matter can be a more appropriate mechanism than autotrophic respiration to explain the relationship between global warming and DIC flux change in rivers. Through the consumption of plankton, the animal life in rivers thus influences the inorganic carbon in groundwaters, creating a negative feedback in the carbon cycle.