It is increasingly well understood that stream communities are regulated by both local niche and regional dispersal processes, but comprehensive tests of these factors with datasets that cover extensive spatial and temporal scales are rare. Based on 1180 benthic invertebrate community samples from 2005 to 2012 in central low mountain streams of Germany, we tested the hypotheses that: 1) local contribution to beta diversity (LCBD: a measure of the uniqueness of communities) would decline with increasing average community dispersal capacity; and 2) owing to the relatively large spatial extent of the study region, regional dispersal processes would override local niche controls in structuring community composition. We found considerable temporal variation in LCBD and a negative correlation between LCBD and community dispersal capacity. However, no statistically significant correlation between species contribution to beta diversity (SCBD) and species dispersal capacity was observed. The large-scale spatial structure among locations (representative of dispersal limitation) was important in structuring benthic communities. Although much of the variation was explained by the shared effects of local processes and large-scale spatial variables, environmental controls were stronger than regional processes in few cases in the variance partitioning analysis, with the annual mean temperature and mean diurnal range of temperature being the important drivers. Given the highly varied correlates of beta diversity over time, we urge researchers to focus on not only spatial variation in diversity, but also the context of temporal variation.