Twenty-six samples from two major altered volcanic ash beds, Kinnekulle and BII Bentonite of the Kuressaare core section (K-3), Saaremaa Island, were explored to record the geochemical and mineralogical heterogeneity of beds. Signs of ash transport fractionation, redeposition of volcanic ash and diagenetic redistribution of material are described and interpreted. In authigenic mineralogy of the Kinnekulle Bentonite illite-smectite dominates with addition of K-feldspar at the margins. The BII Bentonite is composed of chlorite-smectite and illite-smectite. The stability of phenocryst compositions, including that of sanidine and biotite, indicates that both bentonites originate from a single eruption. The observed rather stable pyroclastic sanidine compositions in the cross section of bentonites confirm the reliability of sanidine-based fingerprinting of altered volcanic ash beds. Trace element distribution in bentonites and host rocks indicates that Zr, Ga, Rb, Nb, Ti and Th stayed largely immobile during volcanic ash alteration and reflect primary ash composition. However, some redistribution of Nb and Ti as well as Y has probably occurred near the contacts of bentonite with the host rock. More scattered grain size distribution and immobile element patterns of the Kinnekulle Bentonite support the idea that the primary ash bed had a heterogeneous composition and it was one of the biggest bentonites of the Phanerozoic and most likely records an extended volcanic event. Significant geochemical variations, including a high S content, near the upper and lower contacts of the Kinnekulle Bentonite and elevated Ca and P in host rocks of both bentonites suggest that the studied large ash-falls caused notable perturbations in shallow marine and early post-sedimentary environment.