Dolomite and calcite in Bavarian bentonites, southern Germany, were investigated using petrography, field-emission scanning electron microscopy and stable isotope geochemistry to explore the role of authigenic carbonate formation during bentonitization. Pedogenic, palustrine and groundwater carbonates were distinguished on the basis of X-ray diffraction, micromorphological and stable isotope analysis. The δ13CV-PDB and δ18OV-PDB values of dolomite range from −8.0‰ to −6.1‰ and −5.4‰ to −3.4‰, respectively. Calcites show a range from −11.9‰ to −8.1‰ for carbon and from −9.1‰ to −6.2‰ for oxygen. Carbon isotope compositions imply a C3-plant-dominated carbon source and repeated wetting and drying cycles. The oxygen isotope data points to an evaporation and temperature controlled δ18OV-SMOW value of meteoric water of −7.0‰ to −4.8‰. A syngenetic to early diagenetic timing of dolomitization is indicated, suggesting both dolomite and bentonite formation in non-saline, non-arid and repeatedly partially-oxygenated and reducing soil and groundwater environments during pedogenesis.