The data set bundle comprises geochemical, XRF core scanning and pollen data from composite sediment core BIS-2000, which was compiled from two parallel sediment cores (BIS-1 and BIS-3) obtained near Bispingen, northern Germany (53.071528°N, 9.989861°E, 82.0 m). BIS-2000 comprises Last Interglacial (Eemian) to early Last Glacial (Weichselian) palaeolake deposits, which cover the section between 15.55 and 30.68 m composite depth.The data set Bispingen BIS-2000 pollen contains pollen percentage values of selected taxa. Analyses were carried out at the University of Bonn, Germany, and at the University of the Witwatersrand, South Africa, on the section between 18.19 and 30.68 m composite depth. Sample preparation followed the standard method described by Berglund & Ralska-Jasiewiczowa (1986), including treatment with cool HF and HCl, acetolysis, staining with safranine, and mounting in glycerol. Pollen counting was carried out using a light microscope at 400× magnification and pollen percentages were calculated based on the sum of trees/shrubs (arboreal pollen) and dwarf shrubs/herbs (non-arboreal pollen; excluding aquatic and wetland plants).