We investigated (1) the variation of both species composition and species relative abundances of aquatic beetles associated with submerged woody debris in a transitional region between Cerrado (Brazilian savannah) and Atlantic Forest biomes; and (2) which assembling processes are more associated with the observed patterns, species sorting or mass effects. We hypothesized that the marked differences between Cerrado and Atlantic Forest streams regarding vegetation composition and structure would produce different environmental conditions for stream beetle faunas assembling. We used spatial explicit multivariate techniques to analyze whether metacommunity patterns were more associated with environmental variables, indicating a major role of species sorting, or with spatial variables, indicating intense dispersal. We found distinct communities within each biome in terms of both changes in taxonomic composition and species relative abundance driven by environmental factors. Biome type, a regional scale variable, and variation in dissolved oxygen levels, a local scale variable, were the best explanatory variables of variation in metacommunity structure. We did not find any evidence of the influence of processes related to the spatial configuration of streams. Altogether our results pointed to species sorting structuring saproxylic beetles assemblages patterns.