Small lakes at middle- to high-elevations (1,500-3,500 m asl; hereafter “alpine”) can be sensitive recorders of regional climate change, but these lakes can also be sensitive to local factors. For example, basin morphology of small alpine lakes is known to have a significant effect on the thermal structure of the water column, as well as the duration and spatial extent of winter ice cover. In turn, these conditions may affect the species composition of the diatom flora found in alpine lakes. In an effort to better characterize diatom microfossil variability in alpine lakes, this presentation explores the relationships between lake geomorphology and diatom assemblages. The lakes in this study have been divided into three categories: Type I - shallow (< 1 m deep), flat-bottomed; Type II - deep central basin (>5 m deep), surrounded by a shallow shelf (“inverted sombrero”); and Type III - deep (>6 m deep) with steep sides. Shallow, flat-bottomed lakes are characterized by a diverse benthic assemblage including motile, non-motile, and prostrate epiphytic species. Lakes with a shallow shelf and deep basin are often dominated by tychoplanktonic taxa which form large mats in shallow water. As these mats break up, and the constituent diatoms are then deposited in deeper water. Deep lakes with steep sides are often dominated by planktic diatoms. Therefore, as lake levels change over time, the basin morphology of individual lakes can also change (eg. a lake can begin as a Type I which, over time, becomes a Type III lake as it fills, culminating in a Type II lake), leading to variations in the timing and magnitude of thermal stratification and ice cover, which in turn can lead to changes in the dominant members of the diatom assemblage. The major conclusions from this analysis are that (1) bathymetry in modern lakes affects the composition of the diatom assemblage; and (2) changes in the diatom assemblage can be used to infer past variations in lake levels. Data from lakes in California, eastern Nevada, and Idaho will be presented as examples of modern variability and as potential archives of lake level change.