The question why aquatic communities are often absent in suitable pools still remains a topic of debate and is often explained by dispersal limitation or biological barriers. Cryoconite holes (water‐filled depressions on glaciers) as natural, simple and dynamic habitats in a glacial biome seem to be a good model for addressing this question. The main aim of our research was to investigate links between changes in weather conditions and short temporal changes in invertebrate densities on glaciers. For this study, we selected cryoconite holes on the valley Longyear Glacier and collected samples at two‐day intervals from the same holes in August 2016. During the sampling campaigns, we detected freezing, shrinking and ablation of cryoconite holes. In the samples, we found only two groups of invertebrates, Tardigrada and Rotifera. We observed invertebrates in cryoconite holes until calm weather patterns were interrupted by wind and rainstorm, after which no individuals were detected. Before the storm event, densities in the samples reached up to 149 tardigrades/cm3 and 119 rotifers/cm3 of cryoconite. In addition, we found a strong erosion of cryoconite granules, redistribution into sediments (mud‐like forms), and the migration of granules after rain, which confirmed the mechanical removal of invertebrates by streaming water. Water depth, pH or electrical conductivity did not seem to shape invertebrates communities. Their frequency and densities on valley glaciers depend on stochastic events, for example, weather breakdown (rainstorms). Furthermore, such events may form new niches for tardigrades and rotifers on polar glaciers and influence their coexistence within cryoconite holes.