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Braided rivers are among the most variable and dynamic riverine systems. Changes in these environments are sudden and frequent, driven by the high hydrological variability. They host high levels of local heterogeneity, with many different habitats in close proximity establishing a mosaic of patches. This provides the conditions for high levels of biodiversity, with strong community variability in particular among the different habitats at the stream-reach level. Nevertheless, these systems are still poorly studied and their complexity is often not taken into account in biomonitoring protocols. We applied mixed effects modelling, spatial ordination techniques and beta-diversity partitioning (into nestedness and turnover components) with the aim of improving the knowledge of braided rivers, investigating: i) the organization of macroinvertebrate communities among the different habitats of a river reach, and ii) the temporal variability of this organization (both among seasons and during summer). We predicted a differentiation of macroinvertebrate communities between distinct habitats within rivers, with this differentiation increasing during the low-flow period. We carried out our study in four braided rivers and streams of the Po River basin (Northern Italy) sampling three different kinds of mesohabitats (main channel, secondary channel and pool) in eight stations during seven campaigns from June 2015 to April 2016. We found a high variability of taxa richness, abundance and community structure among mesohabitats, with marginal ones accounting for the greater part of macroinvertebrate diversity. Secondary channels resulted as being the habitat hosting greater taxa diversity, with 10 exclusive taxa. Surprisingly the mesohabitat communities differed greatly during the seasonal phase, whereas their dissimilarity decreased during summer. This could be explained considering the summer flow reduction as a homogenizing force, leading to a general loss of the most sensitive taxa. However, the summer taxa turnover value resulted higher than nestedness, suggesting a strong environmental control on community organization, with taxa well adapted to the different conditions of mesohabitats and able to manage the effects of flow reduction. Our work represents a remarkable issue for biomonitoring protocols, highlighting the importance of taking into account the whole complexity of braided rivers for a more realistic evaluation of macroinvertebrate communities.