The Quincy Diatomite, central Washington, USA, is a middle Miocene (∼ 15 Ma) lacustrine deposit located between flows of the Columbia River Basalt Group. Two primary localities along the western margin of the deposit are examined for stratigraphic and geographic variation. Three lithologic units are recognized in the deposit and are distinguished by distinct diatom florasand subtle lithologic differences. Diatom assemblages vary geographically along the western margin of the basin. Distinctions between these assemblages are confirmed through analysis of point count data using nonMetric Multidimensional Scaling and cluster analyses. Three stages of lake development, directly influenced by the regional geology and geography, are recognized. The earliest stage was likely deposited in a series of small-interconnected pocket lakes that were eutrophic and slightly alkaline. This lake stage was succeeded by a period of shallower water depth, and dominated by benthic species. The latest stage of the lake is interpreted as representing a deepening and expansion of the lake, based on the dominance of planktonic diatom species. Tectonic uplift of the western Frenchman Hills Anticline combined with overall subsidence of the Quincy Basin during intermediate and late stages of lake development is interpreted to be the driver for relative changes in lake bathymetry.