This dataset provides counts of chironomid head capsules for the Lateglacial sediment sequence retrieved from Lake Hämelsee (Germany) in 2013. Counts per taxon are presented against both depth (m) and age (cal yr. BP), and the total amount of material used for analysis (in g) is provided as well. The chironomid data provides information on Lateglacial ecosystem dynamics and were used to interpret changes in aquatic diversity as well as in local climate conditions. A total of 123 samples from the Lateglacial section of the core were treated with warm KOH (10%) to de-flocculate the material and subsequently rinsed through a sieve with a 100-µm mesh. Chironomid head capsules (HCs) were hand-picked from the residue using a Bogorov sorting tray and mounted on permanent microscope slides using Euparal mounting medium. HCs were identified using Brooks et al. (2007) and the dataset presented here has been matched to the taxonomy of the merged Norwegian/Swiss chironomid-climate calibration dataset. Several samples had low chironomid concentrations and for these we amalgamated adjacent samples (within lithological boundaries) to reach a minimum count sum of 50 head capsules per sample. This process resulted in the final chironomid dataset that is presented here, containing 97 samples. All analyses were performed in the laboratories of the University of Amsterdam, the Netherlands.