A 226-cm-long sediment core spanning the past ~ 11,400 years was recovered from Medicine Lake, on the Modoc Plateau in northeastern California. Diatom assemblages provide a record of lake level that is driven by local and regional climate changes and changes in basin morphology due to the activity of Medicine Lake volcano. The diatom record indicates that throughout its history, Medicine Lake was an oligotrophic lake, dominated by Cyclotella stelligera and C. pseudostelligera. Variations in lake level are suggested by changes in the structure of the diatom assemblages. The lowest part of the core (11,400 to 10,300 cal yr B.P.) contains the transition from glacial to interglacial conditions. From about 11,000 to 5500 cal yr B.P., the lake filled two small, steep-sided basins or one basin with two steep-sided sub-basins connected by a shallow shelf. During this time, the diatom evidence (Cyclotella/Navicula ratio) indicates that effective moisture increased, leading to a deeper lake. Over the past 5500 years the diatom record indicates fluctuations in lake level. The change in lake level pattern from one of increasing depth prior to about 5500 cal yr B.P. to one of variable depths may be related to changes in the morphology of the Medicine Lake basin in addition to shifts in local and regional climate. During this latter period the Cyclotella/Navicula ratio varies, suggesting that the level of the lake fluctuated, resulting in changes in colonizable shelf area.