Local conditions, including lake size, depth, bathymetric profile, watershed characteristics, and timing and extent of ice cover determine the characteristics of diatom floras, and how those assemblages respond to short and long-term changes in climate. The diatom assemblages from fourteen sediment samples collected from marginal and profundal zones of seven lakes in the Ruby Mountains and East Humboldt Range of northeastern Nevada are characterized in order to identify the factors affecting controlling species diversity, equitability, and assemblage structure. Principle component analysis delineates three depth-controlled diatom assemblages: shallow (~1), medium (~11 m), and deep (>12 m). The shallowest samples are characterized by a diverse benthic assemblage, the medium depth sample is dominated by small fragilarioid taxa, and, the deepest samples, while not dominated by planktonic species, show an increase in their abundance. In general, diatom assemblages in shallower samples exhibit higher diversity and greater equitability.