AbstractDiatom assemblages from four different substrates from a stream on Byers Peninsula were analysed during the summer. The substrate type was the main factor explaining the variability in the diatom assemblages. Sandy biofilms showed a higher diversity and a greater number of endemic species. Two main hydrological regimes were observed: 1) a hydrologically unstable period with high variability in stream flow and successive freezing and thawing periods, 2) a late summer hydrologically stable period, characterized by low stream velocity and variability. The structure of the diatom communities was different between the two hydrological periods, although the substrate modulated the difference. The diatom assemblages showed low similarity among the substrates and high dominance of endemic species during early summer. The late summer community showed high dominance of motile cosmopolitan species on all substrate types. As the length of both hydrological regimes would ultimately be driven by climatic variability, the predicted climate warming could reduce overall stream diversity. Hence, subtle changes could alter the length of both hydrological periods. The relationship between diatom species association with different substrates and hydrological regimes could be relevant for tracking past climate variability using diatom palaeorecords.