Ecological effects of flooding and drying events are relatively understudied in the Neotropics and less is known about these hydrological extremes in intermittent streams. Neotropical headwater streams in Costa Rica provide opportunities to evaluate the response of macroinvertebrate communities to seasonal changes in flow regime in relatively human undisturbed systems. We quantified the effects of seasonal flow variation on aquatic macroinvertebrate assemblages (i.e., density, richness, and functional traits) within two headwater streams with differing hydrological regimes (i.e., intermittent versus perennial), in the Pacific North of Costa Rica. We sampled macroinvertebrates monthly over a year in riffle and pool habitats. Non-metric multidimensional scaling (NMDS) analyses indicated differences in macroinvertebrate taxonomic richness and density between the two streams and riffle and pool habitats. We found that macroinvertebrates in the intermittent stream riffles had significantly higher richness during the dry season. We also found higher macroinvertebrate functional trait richness in the intermittent stream riffle habitats during the dry season. Our results may be explained by life history traits related to stream velocity preference or tolerance, short life cycles that limit exposure to disturbances, and dispersal capacities and feeding mechanisms that are dependent on water movement.