Description: Diverse benthic communities in streams include a wide variety of predators with different habitat preferences, e.g. for pools or riffles. We hypothesised that these preferences result in mesohabitat-specific predator community structures with quantitative differences concerning predation intensity by vertebrate and invertebrate predators, importance of intraguild predation, or top–down pressure. This hypothesis was evaluated for a small submontane stream by means of mesohabitat-specific quantification of prey consumption by two benthivorous fish species ( Gobio gobio and Barbatula barbatula ) and several invertebrate predators. The estimation was based on daily food rations and diet composition of predators and mesohabitat-specific predator biomass. We found clear differences between the two mesohabitat types. Predator food webs were less complex in pools than in riffles. Fish predation was more important than invertebrate predation in pools, and intraguild predation had a higher relative importance in these mesohabitats. These differences were probably caused by the mesohabitat use of G. gobio , the largest top predator, which preferred pools. Consequently, the predator food webs were more similar between the mesohabitats when fish were absent. Top–down pressure on primary consumers by all predators together was lowest in pools without fish, but the effect was not significant. Omnivory (including cannibalism) was intense, but its potentially destabilising effects were probably counterbalanced by mesohabitat connectivity. From the results of our experimental study, we conclude that even in small stream ecosystems, food web structures and predation pathways can differ between mesohabitats and that a mesohabitat-specific consideration will help to explain the variety of top–down effects on benthic communities.