This dataset provides the raw pollen counts for the late-glacial sediment sequence retrieved from Lake Haemelsee (Germany) in 2013. The counts are presented against both depth (cm core depth) and time (cal. yr BP) and cover the time interval from ca 15.200 to 10.400 cal yr BP. A total of 106 samples were counted, with higher sampling resolution around the onset and end of the Younger Dryas, and lower sampling resolution elsewhere in the core. The pollen record provides information about both regional vegetation change as well as changes in the within-lake flora. It was produced to inform on the exact age and duration of major palynological transitions during the late-glacial Cores were retrieved from the lake using a 3-m long UWITEC piston corer deployed from a floating coring platform during field work in July 2013. Volumetric samples were obtained from splits of the core and processed in the laboratory (University of Amsterdam, the Netherlands) using standard protocols.