Although intermittent rivers are present in all climate regions, their biodiversity and ecosystem functions were largely overlooked in the past. Recently, considerable effort has been made to improve our understanding of these, however, many data gaps still remain. We conducted a study to improve knowledge of the community patterns and processes in intermittent rivers in the Dinaric Western Balkan ecoregion. We studied spatial and temporal variation of aquatic insect community composition and structure in the intermittent Krčić River over two seasons (June and December) in three river sections (spring, upper/middle and lower reaches), encompassing dominant microhabitats (phytal, boulders, cobbles, sand and xylal). Community was primarily composed of aquatic insects (92 % of the community) and seasonality was inferred as the most important factor determining its composition, diversity and abundance. This was also supported by the ecological trait information, i.e. trophic and dispersal-related community structure. The most diverse and abundant insect group were the under-investigated chironomids, thus, we discussed tolerance and intermittency indicator potential of some of these taxa. By providing new insights into temporal and spatial dynamics of aquatic insect communities, a major bioindicator component of the macroinvertebrate community used in water quality monitoring in intermittent rivers, our data support development of the intermittent river-specific and adequate management and monitoring procedures.