Percent abundance of 109 diatom species collected from a Foy Lake (Montana, USA) sediment core that was sampled every ∼5–20 years, yielding a ∼7 kyr record over 800 time-steps. This dataset is associated with the following publication: Angeler, D., T. Eason, A. Garmestani, T. Spanbauer, and C. Allen. Assessing cross-scale patterns and the composition of ecological communities of alternative lake regimes. PLoS ONE. Public Library of Science, San Francisco, CA, USA, 01, (2018).