In Mediterranean climate areas, the great seasonal variability in temperature and rainfall is considered to be an evolutionary pressure that constrains plant and animal communities and their biological traits. Droughts alter habitat availability (changes of flow alter riffle-pool sequences), although habitat characteristics may also exacerbate drought to some extent. Using a simple quantitative index based on the proportion of conglomerate bedrock versus gravel and cobbles, pools versus riffles and winter versus summer flow, we show how habitat characteristics (in terms of substratum and flow) may influence the permanency of a stream site and how flow permanence constrains macroinvertebrate community structure and biological traits. Annual and seasonal macroinvertebrate richness, and the EPT (Ephemeroptera, Plecoptera and Trichoptera) and OCH (Odonata, Coleoptera and Hemiptera) metrics differed between permanent, intermittent and ephemeral sites, but not between permanent and intermittent sites. In contrast, distinct biological traits were observed in the three flow categories, although permanent sites presented few significant traits which was attributed to the stability of the habitat. Intermittent sites were dominated by taxa with pool-like strategies, while ephemeral sites were characterized by fauna with life-history adaptations to floods and droughts. In contrast to most traits (e.g., dissemination, reproduction, substrate relation), which were more constrained by local flow and substrate characteristics, life-cycle characteristics did not differ significantly among flow categories. This pattern can be explained by the features of the Mediterranean climate and particularly its high seasonal predictability, which serves as a large-scale filter of life-cycle traits, independently of local hydromorphological characteristics. Our findings indicate that drought is related to habitat characteristics and that local habitat variability favours organisms with certain traits, while other traits are independent of habitat variability on this scale and are probably affected by other large-scale habitat characteristics.