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The changes in diatom species composition in a sediment core from Crevice Lake, Yellowstone National Park, spanning the past 2550 yr, were used to reconstruct long-term limnological and ecological conditions that may be related to late Holocene climate variability. Planktic forms dominate the fossil diatom assemblages throughout this record, but changes in species dominance indicate varying nutrient levels over time, particularly phosphorus. The changes in the nutrient concentrations in the lake were probably driven by changes in temperature and wind strength that affected the duration of watercolumn mixing and thus the extent of nutrient recycling from deep waters. Prior to 2100 cal before present (BP), Stephanodiscus minutulus and Synedra tenera dominated, suggesting long cool springs with extensive regeneration of phosphorus from the hypolimnion that resulted from isothermal mixing. From 2100 to 800 cal BP, these species were replaced by Cyclotella michiganiana and Cyclotella bodanica. These species are characteristic of lower nutrient concentrations and are interpreted here to reflect warm summers with long periods of thermal stratification. From 800 to 50 cal BP, S. minutulus dominated the diatom assemblage, suggesting a return to lengthy mixing during spring. The most dramatic late Holocene changes in the fossil diatom assemblages occurred during the transition from the Medieval Period to the Little Ice Age, approximately 800 cal BP.