The responses of ecological communities and ecosystems to increased rates of environmental change will be strongly influenced by variation in the diversity of community composition. Yet, our understanding of how diversity is affected by rising temperatures is inconclusive and mainly based on indirect evidence or short-term experiments. In our study, we analyse the diversity and species turnover of benthic epilithic communities within the thermal flume of a nuclear power plant at the Swedish coast. This flume covers the range of predicted future temperature rises. Species composition was significantly different between control sites and sites with higher temperatures. We found that temperature had little effect on the number of species in three functional groups (macroinvertebrates, benthic diatoms, and macrophytes, which here comprise multicellular algae and macroscopic colonies of unicellular algae and cyanobacteria), neither at single sampling dates nor summed for the entire observation year. However, species turnover significantly increased with increasing temperature for diatoms, macrophytes and invertebrates. Different temperature regimes resulted in significantly different species composition and indicator species. Thus, increasing temperatures in the thermal flume increased temporal beta-diversity and decreased compositional stability of communities, although observed richness did not change at any point in time. We highlight the need to investigate the consequences of such declines in compositional stability for functional stability of ecosystem processes.