This dataset provides palaeoecological data for 5 West Midlands Meres (UK). The meres that were sampled are Aqualate Mere, Comber Mere, Cop Mere, Crose Mere, and White Mere. Chironomid counts are presented against depth (cm) and age (year CE). The data provides information on the changes in the lake ecosystem, and has been used to identify the effects of external drivers on biodiversity parameters, with a focus on the effects of eutrophication of shallow meres on alpha and beta diversity dynamics of the chironomid fauna. Sediment cores were retrieved from the respective lakes using gravity corers deployed from a boat, in April 2023. The gravity cores were sampled at (a) the deepest end (30.5-38.5 cm), (b) 10.5 cm, and (c) consecutive 1-cm-thick samples between 0-3 cm core depth. A total of 25 samples from the sediment sequences were treated with warm KOH (10%) to de-flocculate the material, and subsequently rinsed over a 100 µm mesh. Chironomid head capsules (HCs) were picked from the residue using a Bogorov sorting tray, and mounted onto microscope slides using Euparal mounting medium. HCs were identified using Brooks et al., (2007, doi:10.1007/s10933-007-9191-1). Cricotopus (Isocladius) intersectus-type and Cricotopus (Isocladius) laricomalis-type were combined into a single group (C. intersectus-type sensu lato (s.l.)), as they are similar in appearance and ecological role (Brooks et al., 2007, doi:10.1007/s10933-007-9191-1).