We examined the effect of spatial scale on aquatic macroinvertebrate communities in Mediterranean streams from six basins distributed across southern Europe, including Spain, France, Italy, and Greece. We classified the studied streams according to their long-term aquatic regime into the three following types: (i) permanent (P), (ii) intermittent with summer pools (I-P), and (iii) intermittent with summer dry channels (I-D). For each stream type, we analyzed taxonomic and trait diversity, as well as the composition of the macroinvertebrate community, following a spatially nested design at three spatial scales of analysis: microhabitat (substratum patches), mesohabitat (pools vs. riffles), and macrohabitat (streams). In order to assess intrinsic seasonal variability in streams from the Mediterranean region, 20 Surber samples were taken from each stream according to meso- and microhabitat frequency in the wet and the dry season during 2010. Given the need for adaptation to specific hydrological conditions and the fact that microhabitats should encompass the niche requirements of particular taxa, we hypothesized that this spatial scale would have a greater influence on macroinvertebrate taxa composition and biological traits than the other two larger spatial scales in intermittent streams. We observed that patterns in the relative importance of variance components across hierarchical spatial scales changed with time because low flow or droughts altered both mesohabitat preva - lence and microhabitat composition. Our results confirm the importance of the microhabitat scale in I-P streams in the wet season but not in the dry one, when a loss of microhabitat diversity occurred. Stream-to-stream variability was more important in P and I-D streams. Our study also explored the relationships between traits and aquatic regimes. We found that aquatic macroinvertebrates inhabiting permanent streams exhibited traits related to the longer duration of life cycles in these rivers (e.g. large size of adult stages) and adaptations to flowing conditions (e.g. modes of aquatic dispersal), whereas aquatic macroinvertebrates inhabiting intermittent streams with summer pools had traits adapted to depositional conditions and ecological preferences for confined habitats (i.e. disconnected pools without flow). Finally, aquatic macroinvertebrates from intermittent streams with summer dry channels had adaptations conferring ability to survive periods with no water (e.g. modes of aerial dispersal, resistant stages). These results indicate that microhabitat conditions should not be neglected as they can play an important role in certain situations.