Habitat structure is thought to play an important role in ecological communities, with more complex habitat containing higher species richness than simple ones. In the present study, in order to assess the impact of exposed bedrock due to stream straightening on the diversity of stream benthos, invertebrate assemblages on gravel and exposed bedrock were monitored in different seasons. Artificial tiles made of the same granite rock as the bedrock were also used in the field colonization experiments, with contrasting surface complexity (simple and complex). The gravel substrates had higher taxa richness, biomass and number-based Shannon-Wiener diversity index (hereafter H’) of invertebrate assemblages than bedrock ones. The gravel habitat contained three Dipterans (two types of Orthocladiinae and Tiplidae) and two Ephemeropterans (Ephemerellidae and Caenidae), while bedrock was dominated by three Dipterans. Among eight environmental factors of stream ecosystems, two factors　relating to substrate complexity (average and the stand error of substrate size) significantly affected taxa richness and the number-based H’. Complex tiles had significant higher taxa richness and biomass than simple ones in summer season. The results demonstrated that the exposed bedrock had a negative impact on the diversity of stream invertebrate assemblages with apparent faunal simplification.