This dataset provides chironomid counts for the Holocene sediment sequence retrieved from Lake Flocktjärn (Sweden) in 2014. The counts are presented against both depth (m) and age (ka BP). A total of 44 samples were counted. The chironomid counts provide information about changes in the invertebrate fauna of the lake. Cores were retrieved from the lake using a 1-m long handheld piston corer deployed from a floating coring platform during field work in May 2014. Volumetric samples were obtained from splits of the core and processed in the laboratory (University of Amsterdam, the Netherlands) using standard protocols.