This data set provides diatom counts combined from the sediment cores BO10/79 and BO10/81 from peri-alpine Lake Constance. Sediment cores were sampled with a gravity Multi-Corer in May 2010 in the Friedrichshafen Bay (140 m depth). Dating of the laminated cores was done visually using distinct marker beds from large flood events which were derived from runoff data of the Alpine Rhine River. Age estimation of individual samples was done using linear interpolation between marker beds (i.e., 1908, 1922, 1927, 1954, 1971/72, 1987, 2005) and the sediment surface (2010).