Magnesium silicates such as chain clays and Mg-rich interstratifications commonly form in saline and alkaline soil and lake waters. Geochemical analyses of water and sediment from the Lake Eyasi and Ngorongoro Crater watersheds (northern Tanzania) were carried out to test the hypothesis that elevated aqueous CO2 due to biological activity strongly affects the stability of Mg-rich clay minerals. Field data and model calculations show that PCO2 is an important control on pH, thereby affecting mineral stability. Initial supersaturation of water with respect to magnesium clays generally requires elevated pH, and subsequent pH suppression due to biotic CO2 can prevent mineral precipitation. At Ngorongoro and Eyasi, solute Na+, SO42−, Cl, and alkalinity follow generally conservative evaporative enrichment trajectories, whereas solute Ca2+ is lost to calcite, SiO2 to biogenic amorphous silica, and K+ to clay uptake. Mg2+ behavior is highly variable, and does not follow any simple trajectory. Minimal evaporative concentration is required for magnesium silicate supersaturation, and a strong correlation is found between PCO2 and magnesium silicate solubility (Ngorongoro r2=0.70, p<0.001; Eyasi r2=0.61, p<0.001), independent of evaporatively-driven brine evolution. Microbial decay in surface and groundwaters therefore likely plays an important role in the diagenesis of lacustrine clays. Associated ultrafine (<0.1μm) clays show significant Mg enrichment (Mg/(Al+Fe)=1.5–4.0) compared to <0.1μm detrital source clays (Mg/(Al+Fe)<0.1), and have an intermediate average chemistry between aluminous dioctahedral clays and end-member trioctahedral smectites or kerolite. The kinetics of magnesium clay precipitation remain poorly understood, but the preservation of such clays in ancient deposits may represent not only paleo-solution salinity and alkalinity, but also CO2 gas equilibrium status. These diagenetic processes should be considered in the use of lacustrine clay minerals as paleochemical indicators, because diagenetic pH suppression in sub-lacustrine pore waters can effectively remove indicators of high paleo-salinity

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