We examined the effects of interstitial space between stream substrate particles on the colonization of aquatic organisms using three types of substrates (gravel, a cobble, and a cobble on gravel) in a riffle and pool of a temperate stream. Significantly greater abundance, wet weight, diversity (H′), taxonomic richness, and evenness of aquatic organisms were found in the riffle than in the pool, and the interstitial space substrate (i.e., a cobble on gravel) had significantly greater abundance, wet weight, and taxonomic richness of aquatic organisms than did the cobble substrate. Of the 13 families observed in the experiments, larval net-spinning caddisfly (Hydropsychidae) dominated the riffle in terms of the abundance and wet weight; chironomid larvae dominated both the riffle and the pool in terms of abundance. Simple main effect tests indicated significant effects of substrate on the abundance and wet weight of larval caddisfly in the riffle, and post hoc tests on substrate in each habitat indicated that the abundance and wet weight of larval caddisfly on interstitial space substrate were significantly greater than those on cobble substrate in the riffle. Our results suggest the importance of interstitial space between stream substrates in riffles to ensure higher colonization rates of aquatic organisms such as larval net-spinning caddisflies characterized as filter feeders.