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.