In the late 1980’s and early 1990’s, various media in karst environments in the Northern Yukon Territory were examined for their diatom content. Cryogenic cave calcite powders, grus and various ice formations (ice plugs, ice stalagmites and floor ice) were collected from three freezing caves and one slope cave to make an inventory of the diatom content, and to explain the spatial distribution of the diatoms within the caves. The results show that approximately 20% of diatoms in the caves originate from external biotopes and habitats (e.g., river, lake, stream), with the remaining 80% of local origin (i.e., from subaerial habitats near cave entrances). The results also indicate that the greater abundance of diatoms is found in the larger caves. This is explained by the fact that the air circulation dynamics are much more important in caves that have a larger entrance. Also grus, ice plugs and ice stalagmites have the lowest diatom diversity, but greater relative abundance, indicative of growth in specific habitats or under specific conditions. Overall, these results are a contribution to the study of particles transport in ice caves.