This dataset provides palaeoecological data for 8 sites across the Lake District (England) and Scotland. Chironomid counts are presented against depth (cm), composite 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 (alpha and beta diversity). The lakes were selected based on the identification of, insofar as possible, a single driver acting on the lakes, based on their known histories and existing palaeoecological studies. Existing cores were used where available, for direct comparison with existing (primarily diatom) data. Additional cores were taken in 2024 from the sites where access was possible to extend the record of observation to the present. Butterstone Loch was cored in 1998 as part of an investigation into Scottish freshwater Lochs (Bennion et al., 2004; doi:10.1111/j.1365-2664.2004.00874.x). Derwent Water, Esthwaite Water, Grasmere, and Rydal Water, in the Lake District, England, and Bishop Loch, Loch Libo, and Woodend Loch, in Scotland were cored in 2016 as part of the Hydroscape project (Willby et al., 2019). These cores were collected using a combination of Tapper (Chambers & Camerson, 2001; doi:10.1023/A:1008181406301), HON-Kajak (Renberg, 1991; doi:10.1007/BF00153740), and Big Ben (Patmore et al., 2014; doi:10.1007/s10933-013-9756-0) corers. The sampling strategy for these cores was as follows: (a) a sample taken from the deepest part of the record; (b) an approximate midpoint sample; and (c) continuous 1-cm-thick samples taken between 0-3 cm core depth. This sampling strategy was modified when insufficient material was available. Additional samples were taken from periods of interest, e.g. Esthwaite Water was sampled at 20 cm and 14.5 cm to capture the opening of the Sewage Treatment Works (1973 CE) and the modification of the filtering process (1986 CE), respectively. Additional cores were collected in April 2024 from Butterstone Loch, Derwent Water, Grasmere, and Loch Libo, using gravity corers (Boyle, 1995, doi:10.1007/BF00678113). The 2024 cores were combined with the existing 1998 and 2016 cores, to create continuous profiles covering the past few centuries and up to the present day. Depth was adjusted based on sedimentation rate to create composite depth (cm) profiles. The 2024 cores were sampled at the surface (0-1 cm core depth). Three additional samples were taken from the BUTT24 core (3.5 cm, 6.5 cm, 9.5 cm) due to the longer interval since initial sampling in 1998 CE. A total of 49 samples from the combined 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. HCs were mounted on 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.)), due to their similarity in appearance and ecological role (Brooks et al., 2007; doi:10.1007/s10933-007-9191-1). Where appropriate, datasets were processed through amalgamation of consecutive samples in order to e.g. ensure high count sums.