The need to understand the influence of high-level factors that shape species richness and population size is becoming more important as global biodiversity losses threaten biotic communities. Here we investigate the influence of ecological drift on periphytic diatom community composition in arctic lakes. If community composition is strongly influenced by drift, we hypothesize that (i) alpha diversity will increase with increasing lake size, due to the decreasing influence of drift-mediated local extinction, (ii) beta diversity will be greatest among small lakes and lowest in large lakes, and (iii) relationships between community size and environmental variables will be strongest in large lakes and weakest in small lakes. Analysis was conducted on periphytic diatoms accrued on artificial substrates in 44 shallow, thermokarst lakes over the 2009 growing season. Limnological and hydrological conditions at each site were described and their influence was removed to minimize the confounding effect of environmental heterogeneity. Alpha diversity was not significantly different among the lake sizes. Total beta diversity was significantly higher in the small lakes than the medium lakes. Beta diversity was primarily attributed to turnover, and small lakes had significantly higher turnover than medium and large lakes, while nestedness was not significantly different among lake-size classes. Periphytic diatom community composition and environmental variables were not significantly concordant in any lake-size class. Our results suggest that drift, as related to habitat size, is not a primary driver of periphytic diatom community composition in shallow, thermokarst arctic lakes.