Benthic diatoms form a particularly important community in oligotrophic lakes, but factors influencing their distribution are not well known. This study reports the depth distribution of living motile and total diatoms (living plus dead diatoms) on both natural (from sand to fine organic mud) and artificial substrates in an oligotrophic lake. On artificial substrates, motile diatom densities peaked in abundance (24–30 cells · mm−2) between 0.6 and 1.9 m depth; on natural sediment surfaces, motile diatoms were generally more numerous and peaked in abundance (925 cells · mm−2) at 1.3 m depth. Total diatom densities on artificial substrates were highest (1260 valves · mm−2) at 0.6 m depth, with very low values below 3 m depth; on natural sediment surfaces, total diatom abundances were generally much higher (21600 valves · mm−2) at 3 m depth and declined gradually with depth. Significant relationships were found between light and diatom densities on the artificial substrate. Ordination analysis indicated that substrate type significantly correlated with the variation of diatom composition on artificial and natural substrates. Our results suggest that in oligotrophic lakes, light influences benthic diatom abundance, whereas substrate type has more influence on benthic diatom composition.