Tectonic basins can represent valuable archives of the environmental history. Presented here are the stratigraphy and multi-proxy analyses of two adjacent alluvial fans in the Quaternary active parts of the Vienna Basin, situated at the interface of the Atlantic, European continental and Mediterranean climate. Deposits comprise a sequence of coarse-grained fluvial deposits intercalated by laterally extensive horizons of pedogenically altered fine sediments. To establish palaeoenvironmental reconstructions, fine-grained sequences from a drill core and outcrop data were analysed according to its malacofauna, palaeopedology, susceptibility and sedimentology. The chronological framework is provided by 38 luminescence ages and supported by geomagnetic polarity investigations. Distinct warm periods each associated with a geomagnetic excursion, are recorded in three pedocomplexes formed during the Last Interglacial and two earlier interglacial periods, indicted to correlate with Marine Isotope Stage (MIS) 9 and MIS 11, respectively. Environmental conditions during the early last glacial period (MIS 5, c. 100–70 ka) are reconstructed from mollusc-shell rich overbank fines deposited along a former channel belt, covered by massive sheetflood deposits during MIS 2. Analysed warm phases suggest strong variations in humidity, ranging from steppe to forest dominated environments. The study presents one of the few numerically dated Middle Pleistocene multi-proxy records and one of the most comprehensive malacological datasets covering the early phases of last glacial period of continental Europe.