Context A better understanding of the use of different trophic pathways as a mechanism for adjusting interactions between coexisting omnivorous decapod species may help define the extent of their influence on energy flows in freshwater ecosystems. Aims Analyse the patterns of use of the benthic and littoral pathways by Macrobrachium borellii and Palaemon argentinus during a hydrological cycle in lakes of the middle Paraná River. Methods The study was conducted during one high-water (HW) and one low-water (LW) period in three lakes permanently connected to the middle Paraná River. We calculated the relative contributions of potential basal resources (benthic and littoral) to each species for each lake and hydrological period using mixing models. Key results It was observed that M. borellii feeds more in the littoral pathway and P. argentinus in the benthic pathway, especially in low water where we observed that the partitioning of resources was more pronounced. Conclusion The more aggessive species, M. borelli, during HW period quickly utilises the bioavailable material. Trophic dynamics and resource use are part of the coexistence mechanisms of both decapod species. Implications This may have important consequences in the aquatic trophic webs in which these organisms participate, because when segregating the use of resources, they intervene in different energetic pathways.