Lacustrine carbonates formed in rift settings are increasingly studied not only as archives of Earth chemical and climatic history but also as potential hydrocarbon source rocks and/or reservoirs. The role of magmatic gases in their formation and diagenetic evolution, hence in their reservoir properties, remains unclear. We studied the first meter of carbonate sediment of the Dziani Dzaha volcanic crater lake (Mayotte Island) and developed a reactive-transport model with CrunchFlow software that allows the quantification of diagenetic reactions by considering depth-dependent burial rates and sediment compaction. The model is constrained by the previously documented solid-phase compositions of the lake sediment and new data consisting of 14C dating of plant macroremains to characterize the sediment age model, chemical composition of sediment pore waters, and chemical and isotopic composition of gases dissolved and bubbling through the lake. These new data reveal a massive magmatic CO2 contribution to the dissolved inorganic carbon of the lake, which fuels the primary productivity and carbonate formation. A pH value of 9 in the surface sediment pore waters induces supersaturation relative to aragonite, hydromagnesite, and saponite. At 1 m depth in the sediment, our model predicts that magmatic CO2 inflows and organic matter degradation account for 22 and 2 mol % dissolved inorganic carbon, respectively. The magmatic CO2 inflows result in a pH decrease at depth, leading to the destabilization of hydromagnesite, while saponite and aragonite remain stable. These results demonstrate the role of magmatic CO2 in fueling carbonate production and controlling the diagenetic evolution of sediment mineralogy.