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Sediment cores and high-resolution bathymetric and seismic reflection data were collected from the lake during the fall of 1999 and 2000. Sediments were analyzed for diatoms, pollen, density, grain size (sand/mud ratio), total organic carbon (TOC), and micro-scale fabric analysis. Using both\u00a014C (AMS) dating and tephrochronology, the basal sediments were estimated to have been deposited about 11,400\u00a0cal\u00a0year BP, thus yielding an estimated average sedimentation rate of about 20.66\u00a0cm/1,000\u00a0year. The lowermost part of the core (11,400\u201310,300\u00a0cal\u00a0year BP) contains the transition from glacial to interglacial conditions. From about 11,000\u20135,500\u00a0cal\u00a0year BP, Medicine Lake consisted of two small, steep-sided lakes or one lake with two steep-sided basins connected by a shallow shelf. During this time, both the pollen (Abies/Artemisia\u00a0ratio) and the diatom (Cyclotella/Navicula\u00a0ratio) evidences indicate that the effective moisture increased, leading to a deeper lake. Over the past 5,500\u00a0years, the pollen record shows that effective moisture continued to increase, and the diatom record indicates fluctuations in the lake level. The change in the lake level pattern from one of the increasing depths prior to about 6,000\u00a0cal\u00a0year BP to one of the variable depths may be related to changes in the morphology of the Medicine Lake caldera associated with the movement of magma and the eruption of the Medicine Lake Glass Flow about 5,120\u00a0cal\u00a0year BP. These changes in basin morphology caused Medicine Lake to flood the shallow shelf which surrounds the deeper part of the lake. During this period, the\u00a0Cyclotella/Navicula\u00a0ratio and the percent abundance of\u00a0Isoetes\u00a0vary, suggesting that the level of the lake fluctuated, resulting in changes in the shelf area available for colonization by benthic diatoms and\u00a0Isoetes. 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