The dataset comprises counts of four planktonic diatom taxa collected from Loch Leven from 1968-2007 by staff at the Centre for Ecology & Hydrology and its predecessor bodies, as part of their long-term monitoring programme of the lake. Count units are the density of cells per millilitre of water for four species; Asterionella formosa, Aulacoseira spp, Diatoma spp, Unicellular centric diatoms. Counts are of weekly to monthly frequency and from a single sampling station Full details about this dataset can be found at https://doi.org/10.5285/de5ca6cc-02e9-42bc-a39e-80ec8acbffba