This dataset provides counts of chironomid taxa identified in a set of surface sediment samples taken in the region around the town of Kaamanen (Finland). A total of 33 lakes were sampled during field work in August 2006. For each lake, a short sediment core was retrieved from a rubber dinghy using a gravity corer (HON/Kajak corer) with a 62mm diameter. Volumetric samples taken from the 0-1cm sediment depth sample were subsequently processed in the laboratory (Vrije Universiteit Amsterdam, the Netherlands) using standard protocols – this involved 20min treatment with warm KOH (10%) and sieving over a 100um mesh. Chironomid head capsules were subsequently handpicked from the residue, mounted on permanent microscope slides, and identified using the literature. This dataset provides chironomid counts per sample as well as longitude, latitude, elevation and measurements of water depth for each of the samples. Engels et al. (2008) provide additional environmental observations (water temperature, conductivity, pH and O2 profiles) for each of the lakes sampled, as well as water chemistry data. The lakes were either situated on the floodplain of the Muddusjoki river and prone to annual flooding, or they were situated at higher elevations and were isolated from fluvial activity. The chironomid dataset was used to determine the effects of regular inundations on the composition of the chironomid fauna of shallow lakes, as well as to determine the effects on chironomid-inferred July air temperature estimates.