This dataset comprises the core data and the 3.5 kHz seismic data of Millstätter See, a lake in the Eastern European Alps, Austria. Together with a bathymetric dataset (10.5281/zenodo.5875923) and a core/seismic dataset from Wörthersee (10.5281/zenodo.5875576), this is the basis for the publication Daxer et al. "High-resolution calibration of seismically-induced lacustrine deposits with historical earthquake data in the Eastern Alps (Carinthia, Austria)". 28 core sections (individual short cores or sections of long cores - see MillstaetterSee_core_data.xlsx for information) were analysed with a multi-sensor core logger (MSCL) and photographed with a smartcube camera image scanner and an ITRAX core scanner. The generated data are available in the folders MSCL.zip and Photos.zip. Some core sections were also analysed with a Malvern Mastersizer 3000 and/or CT scanning. The generated data are provided in the folders Grain Size.zip and CT data MI17-04.zip (as .dcm files). The seismic profiles are provided as .SGY files (Seismic Pinger Data.zip).