Different environmental preferences and dispersal abilities allow fish to coexist in local communities. In the present study we analysed the effects of engineering species on the community structure based on the example of the European beaver (Castor fiber) and mountainous European stream fish. We hypothesised that the creation of beaver impoundments increases environmental heterogeneity and causes a strong spatial and temporal variation in fish species composition and size structure. Finally, we placed these results in the context of the metacommunity theory. Our research was conducted over a large spatial scale, and over a relatively long (5-year) temporal scale. Data analysis revealed strong environmental gradients associated with stream size and increased environmental heterogeneity associated with the creation of beaver impoundments. The results also indicated strong spatial and temporal variation in fish species composition and size structure associated with this environmental heterogeneity. Although local communities changed over time, the main metacommunity characteristics remained constant. Fish must move and follow environmental changes for their populations and communities to persist in streams inhabited by beavers. Gaining a deeper understanding of the effects of the engineering species on fish community structure may help inform management and the conservation of stream ecosystems.