Fossil pigments were examined in a 22 m core of varved sediment from the deep basin of Elk Lake, Minnesota. The lake appears to have evolved gradually from oligotrophic mesotrophic conditions in the earliest period (ca. 10,000+ years ago), to mesotrophic eutrophic conditions at present. Variations in productivity, species diversity, and relative importance of individual plant groups are related to changing climate and water level. The cyanobacteria gradually became more important in the planktonic flora; the least biomass and greatest variation occurred during the first 1000 years of the lake’s postglacial history, and again during the mid-Holocene prairie interval. The ratio of chlorophyll derivatives to carotenoids indicates that there were no periods of large-scale influx of allochthonous detritus, nor were there major slumps of littoral detritus into the deep profundal zone. In addition, there is no evidence to indicate that excessive drying of the lake occurred during the mid-Holocene prairie interval.