Floods and droughts are 2 of the most influential factors affecting the structure and function of benthic macroinvertebrate assemblages in stream ecosystems. Even if these natural disturbances occur at the same magnitude at multiple research sites, the responses may differ according to stream type. In our study, we examined the various responses of functional feeding guilds (FFGs), related to the feeding methods and food types of macroinvertebrates, and habit trait guilds (HTGs), related to the mobility of macroinvertebrates and location of food obtained, to floods and droughts in different stream types (perennial, intermittent, or ephemeral). The stream types were categorised according to the stream flow conditions, flow permanence, and stream connectivity. Perennial streams were those maintaining continuous lotic habitats; intermittent streams were lotic habitats during periods of heavy rain but either connected or isolated pools during dry periods; and ephemeral streams existed only during the rainy season. Among the substrates, cobbles and boulders were highly dominant during heavy rain, especially in the first periods of heavy rain, whereas silt and sand were more often present in high proportions at intermittent stream sites. Across all stream types, highly intense and heavy rain led to a decrease in species richness and abundance, with changes in the composition of both FFGs and HTGs. Organisms characterised as scrapers and/or clingers (e.g., Ecdyonurus dracon, E. levis, and Simuliidae sp.), were highly resistant to high discharge compared to other FFGs or HTGs and were dominant during floods. In dry periods, the composition and richness of FFGs and HTGs were more affected at intermittent streams than at perennial streams. Long-lasting dry periods consistently reduced lotic habitat abundance and diversity and increased the amount of lentic habitats as well as zones with sedimentation, especially at intermittent stream sites, resulting in a decrease in collector-filterer organisms and an increase in burrowers (e.g., Ephemera strigata). Despite seasonal predictability, however, floods of relatively lower magnitude and intensity provided opportunities for some species, especially clingers (e.g., Epeorus pellucidus) and swimmers (e.g., Baetis fuscatus), to be introduced and/or become established in new habitats downstream in the ephemeral streams. Our research indicated that spatial (i.e., stream type) and temporal (i.e., floods and drying events) heterogeneities are the defining factors that influence functional diversity in benthic macroinvertebrate communities.