This dataset provides counts of diatom valves 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). The diatom data provides information on Lateglacial ecosystem dynamics and the dataset was used to interpret changes in aquatic diversity as well as in palaeolimnological conditions. A total of 78 samples were selected for diatom analysis using 2-5 cm sample intervals throughout the Lateglacial section of the core sequence, with a higher sampling resolution (1 cm intervals) around key transitions. Organic matter was removed from the samples (ca. 0.01 grams dried sediment) by oxidation using 5 ml of H2O2 (30%) and heating in a water bath at 70 °C for 24-28 hrs. Subsequently, a few drops of HCl (50%) were added to remove residual H2O2 and carbonates. Samples were washed by adding distilled water, shaking vigorously, centrifuging at 1200 rpm for 4 minutes, and removing the liquid using a pipette. This process was repeated 5 times, and a few drops of ammonia (NH3) were added to the solution prior to the final wash to prevent clumping of diatoms. Diatom slides were mounted using Naphrax and diatoms were identified using Krammer and Lange-Bertalot (1986–1991) and Camburn and Charles (2000). For several samples the target count sum of 300 diatom valves could not be reached due to low concentrations or poor diatom preservation. Prior to analysis and interpretation, and where possible, neighbouring samples with a low count sum were amalgamated until a count of at least 100 valves was reached; if this was not possible the samples were deleted from our dataset prior to subsequent analysis (note that these samples are still included in the dataset provided here). All analyses were performed in the laboratories of University College London, UK.