Macrophytes have a fundamental structuring role in aquatic environments. Several authors have suggested that trophic interactions are particularly mediated by aquatic plants. In the current article, we evaluated the effects of the structural heterogeneity provided by Eichhornia azurea (Kunth) roots on predation and habitat use by the small fish Moenkhausia sanctaefilomenae (Steindachner). We tested the hypotheses that (i) high structural heterogeneity protects macroinvertebrates against predation by M. sanctaefilomenae; (ii) distinct prey types are differently protected by the refuge provided by roots; and (iii) the behavior of M. sanctaefilomenae is affected by the structural heterogeneity provided by macrophyte roots. To test these hypotheses, we performed an experiment in 20 l aquaria in which macroinvertebrates (Cypricercus sp. and Chironomus sp.) were exposed to M. sanctaefilomenae predation for 4 h under three structural heterogeneities, represented by different root densities. High structural heterogeneity protected macroinvertebrates against predation. Additionally, E. azurea roots similarly protected different prey species. The macrophyte spatial structure substantially changed the habitat use of M. sanctaefilomenae. In general, our results corroborated the hypothesis that the structural heterogeneity provided by E. azurea roots significantly affects predation and habitat use by M. sanctaefilomenae.