This dataset provides Pediastrum data for the Lateglacial sediment sequence retrieved from Lake Hämelsee (Germany) in 2013. Percent-abundances per taxon (%), total count sum per sample (#/ml) and Pediastrum flux (#/cm²/a) are presented against both depth (m) and age (cal yr. BP). The Pediastrum 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 dataset of lateglacial pollen samples from lake Haemelsee (see https://doi.pangaea.de/10.1594/PANGAEA.939693) was additionally analysed for subfossil remains of Pediastrum, where identification of the Pediastrum taxa mainly followed Komárek and Jankovská (2001) with further taxonomic revisions as summarized in Turner et al. (2014). Our final Pediastrum dataset includes 100 samples, as samples with fewer than 25 identified Pediastrum coenobia were excluded from further analyses. Pediastrum concentrations were calculated by comparing the number of Lycopodium spores encountered during pollen analyses to the number of spores added to the sample. All analyses were performed in the laboratories of the Technische Universität Braunschweig, Germany.