Abstract Deforestation affects freshwater assemblages since aquatic organisms are dependent on the structure of the riparian vegetation. To investigate the responses of riffle beetles (Elmidae) to deforestation, this study assessed the structure of riffle beetle assemblages found in streams running through a large and well-preserved semi-deciduous Atlantic Forest remnant in Southern Brazil and in nearby deforested areas. Additionally, the effects of different substrate types (litter and stone) on the assemblages were assessed. Riffle beetle assemblages showed a remarkably distinct structure between forested and deforested areas. Lower abundance occurred in deforested streams. Indicator genera of forested streams were detected (e.g.,Macrelmis and Microcylloepus), while a generalist genus (Heterelmis) predominated in deforested streams. Substrate type did not affect the composition of riffle beetle genera, although higher abundance was found in litter. Our results are likely associated with changes in the vegetation type and levels and quality of allochthonous material input between forested (native and higher levels) and deforested (exotic and lower levels) streams, which are directly linked to the feeding habits of riffle beetles. Thus, our study reveals an interesting potential of riffle beetles as indicators of stream ecological integrity in semi-deciduous areas of the Atlantic Forest biome.