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Theory predicts that morphological and bioenergetic constraints due to temperature‐induced body size reduction can modulate the direct effects of warming on biotic interactions, with consequent effects on trophic cascades and biomass distribution. However, these theoretical predictions have rarely been tested empirically. Our aim was to distinguish the indirect effects of warming‐induced body size reductions from the direct effects of warming on community structure. We conducted a mesocosm experiment manipulating factorially 1) body size reduction in the medaka fish Oryzias latipes using two populations raised for several generations under contrasted climate conditions and 2) warming (+4°C), to test their independent and interactive effects on the structure of prey and primary resource communities, the predator–prey biomass ratio and the biomass size spectra. We further dissected the effects of seasonal temperature variation from the effects of constant artificial warming. We found that the indirect effects of warming (i.e. fish body size reduction) on composition and structure of communities as well as their biomass size spectra were of marginal amplitude compared to the direct effects of seasonal temperature variation and constant warming. There were no changes in community composition in response to fish body size reduction or constant warming. However, the density of macroinvertebrates and zooplankton were maximal at intermediate seasonal water temperatures and lower in constantly‐heated mesocosms. Contrastingly, phytoplankton was not strongly affected by seasonal temperature or warming, but rather responded to grazing effects of zooplankton. Finally, we found a reduction in predator–prey biomass ratio under warming and at the warmest seasonal temperature, inducing a steeper slope of the biomass size spectra under increasing seasonal (but not constant) temperature. We conclude that the direct effects of climate change on freshwater communities are stronger than its indirect effects mediated by body mass reduction. [ABSTRACT FROM AUTHOR]