The benthic community of a braided reach of a lowland river was studied with the aim to identify functional habitats through the assessment of potential habitats. Functional habitats were defined considering physical and biological characteristics. Three reaches of the Chocancharava River (Córdoba, Argentina) were selected and six potential habitats were sampled during high and low water periods. Hydraulic and environmental variables were also registered in each sampling occasion. Taxonomic composition, macroinvertebrate abundance, richness, diversity and evenness were estimated for each identified functional habitat. TWINSPAN analysis was applied separately for two data sets (high water and low water period). This analysis showed that samples of the low water period were mainly grouped in relation to three habitats units: vegetated habitats, unvegetated habitats and habitats related to bars. These three habitats were considered functional habitats. The whole biological and environmental data sets were ordinated by Canonical Correspondence Analysis (CCA) showing a significant relationship between benthic assemblages and environmental variables. This analysis grouped samples in relation to the functional habitats identified by TWINSPAN and indicated that the most influential environmental variables explaining the ordination were: current velocity, depth, substrate size and cover percent of rooted emergent macrophytes. Faunal composition determined by CCA for each functional habitat was in agreement with the results obtained by the Relative Preference Index (RPI). Factorial ANOVAs showed that abundance, taxonomic richness, diversity and evenness were different among the functional habitats and that the community attributes were influenced by the effect of the hydrological period and habitat. As the functional habitat approach provides useful tools in management and river rehabilitation the use of this methodology may allow to develop more appropriate restoration strategies to be applied in altered lowland reaches.