Resumo. Abstract Aim Our objective was to describe the structure and spatial patterns of the zooplankton community in a small Brazilian river system (Paranaíba River sub-basin) and evaluate the role of an oxbow lake in the dynamics of this community. Methods Zooplankton samples were collected from sites located in an oxbow lake and the Aporé River bed during the rainy and dry seasons. We collected these samples from the surface and bottom levels of two different zones (littoral and channel). For each hydrological season, analysis of variance was conducted to determine the differences in species richness and abundance of zooplankton among different sites (longitudinal), zones (lateral), and depths (vertical). Cluster analysis was performed to assess the similarity in species composition. In addition, a canonical correspondence analysis was used to select the environmental variables that best explained the variation in zooplankton abundance data. Results We recorded 152 species: 70 rotifers, 53 testate amoebae, 20 cladocerans, and 9 copepods. We observed changes in the species richness and abundance of zooplankton along the longitudinal axis of the river in both the rainy and dry seasons. However, we did not detect any lateral or vertical changes in these attributes. Cluster analysis also indicated that the greatest differences in species composition were in the longitudinal axis of the river. The longitudinal variability of zooplankton was mainly associated with the influence of an upstream oxbow lake, as well as the changes in water flow velocity, turbidity, and concentrations of suspended solids downstream. Conclusions Our results demonstrate the importance of a heterogeneity of hydrological characteristics as a structuring factor of the zooplankton community in the Aporé River. Thus, we highlight the relevance of actions to protect and maintain the natural characteristics of these environments.