Aquatic macroinvertebrates living in anastomosing lowland rivers use different habitats and respond differently to the hydrological regime. In this paper, the structure and composition of benthic, drifting and marginal macroinvertebrate assemblages are analyzed in the lowland river Ctalamochita (Co´rdoba, Argentina). The assemblages were studied in an annual cycle; a comparison among the composition of benthos, drift and marginal fauna was carried out; and size structure of the assemblages was characterized. Samples were obtained from two sites: a rural and an urban site. In total 73 taxa of aquatic macroinvertebrates were collected. Benthos was characterized by Chironomidae and Oligochaeta; marginal fauna was mainly constituted by Coleoptera, Heteroptera, Decapoda, the Trichoptera Nectopsyche sp., Ephemeroptera and Odonata. Drifting assemblage was composed by macroinvertebrates from local and remote upstream benthos, and from the marginal zone. Marginal fauna diversity was higher than benthos and drift. Total biomass of the assemblages pooled together was relatively equitably among size classes. Larger size classes consisted of organisms from the marginal zone whereas the smallest ones were composed by benthic and drifting organisms. In the study area there is habitat partitioning in the lateral dimension of the river. Marginal fauna was more diverse due to the asymmetry of transport and deposit processes, which generate a heterogeneous habitat in the bankside. The relation between fine substrate and high current velocity determines an unstable habitat in the central channel, which makes colonization by benthic macroinvertebrates difficult.