A comprehensive assessment of stream restoration success should link changes in habitat structure not only to changes in taxonomic diversity, but also to functional diversity that affects ecosystem functioning. In this study, we compared the taxonomic and functional composition of periphytic ciliates between restored and unrestored (control) streams for two different immersion periods to: i) identify species with indicator potential ; ii) identify functional traits that differ between the two stream types ; and iii) examine the effects of environmental parameters on species and functional trait composition. In addition, we compared the two stream types in terms of microhabitat heterogeneity through the deposition of organic and inorganic matter (tufa). The periphyton of restored streams is colonized by species that reach high abundance not only in inland waters but also in soil, such as Platyophrya vorax, which was identified as a potential indicator species for restored streams of the Skradinski buk barrier, which has implications for the importance of carbon cycling and organic matter cycling in restored streams. In restored streams, better competitors prevail, i.e., omnivorous, and bacterivorous free- swimming ciliates that utilize a wider range of different niches created by the greater complexity of the microhabitat due to leaching of the surrounding soil, precipitation of calcite crystals, i.e., tufa, and retention of allochthonous organic matter particles. The relationship between microhabitat heterogeneity, ciliate functional traits and organic matter dynamics suggests that stream restoration affects ecosystem functioning through its influence on functional components, suggesting that restored streams are the link between terrestrial and lotic ecosystems.