Recent studies established the lithological and chemical sediment evolution in the Lower Austrian Molasse Basin (LAMB), a part of the North Alpine foreland basin, during the Early Miocene. In this study, we aim to integrate the clay mineralogy of seven wells across the LAMB with a newly proposed lithostratigraphy, and to infer implications for provenance, palaeo-geography and palaeoclimate. The results of our qualitative and quantitative evaluation of the clay-sized fraction with x-ray diffractometry largely support the stratigraphic model. The early stage of foreland basin formation (Egerian/Eggenburgian?) is represented by kaolinite contents up to 93 % in the clay sized fraction. This indicates an orogen-external source, i.e. the Bohemian Massif, and erosion of intensively chemical weathered products during this early Molasse basin stage. The over-lying marine Robulus Schlier (lower/middle Ottnangian) is characterized by a distinctly reduced kaolinite content and overall increased illite content compared to the other formations. Illite was predominantly provided from denudation of the rising Eastern Alps, i.e. characterizing the orogen-internal provenance. The pelites of the overlying carbonate poor Traisen Formation (upper Ottnangian) show again a higher kaolinite and smectite content. In the largely coeval basinal Wildendürnbach Formation, smectite reaches up to 70 % in the clay sized fraction. Peak smectite values may be linked to volcanic ash input from the nearby Carpathian volcanic arc. Generally rising smectite versus illite ratios during the Ottnangian-Karpatian could point to a warming and intensified chemical weathering of the rising Alpine orogen.