Mediterranean streams exhibit highly variable inter-annual and seasonal discharge patterns, exerting an evolutionary pressure that constrains biological communities. Due to climate change, including a decrease in summer rainfall, and concurrent water resource pressures, stream intermittence is increasing in the Mediterranean Basin. In this context, I explored the potential of benthic invertebrate taxa and their biological traits to be used as indicators of different hydrological conditions. I characterized the flow intermittence gradient along a small Mediterranean stream into three aquatic regimes: perennial (P), intermittent with summer pools (IP), and intermittent with dry channels (ID). Then, I compared the performance of taxonomic and trait-based approaches in characterizing the effects of flow intermittence on benthic invertebrate community patterns in two sampling periods: (1) during the flowing period, when pool-riffle sequences were well-established, and (2) during the dry phase, when either isolated pools or dry channels occurred at the intermittent sites. Both the taxonomic and trait composition of communities differed among sites according to their aquatic regime, especially ID sites, which differed considerably from P and IP sites. Organisms from ID sites were characterized by life-history adaptations to flow intermittence (e.g. short life cycles, resistant forms). No significant difference in traits or taxa was observed between P and IP sites in either sampling period. The trait-based approach was a more sensitive indicator of the aquatic regime, emphasizing the need to conduct further research into the development of trait-based biomonitoring and conservation tools for intermittent streams.