Habitat complexity may stabilize consumer–resource interactions and reduce the probability of invasion in aquatic habitats. We tested the hypotheses that (i) higher habitat complexity reduces resource consumption independently of grazer species, but that (ii) invasive grazers have a greater influence on decreasing resources independently of habitat complexity. We performed an experiment using artificial substrates to simulate different complexity levels. We evaluated Melanoides tuberculata (O.F. Müller, 1774) and Aylacostoma chloroticum Hylton Scott, 1954 consumption of specific algal groups and the interaction between habitat complexity and grazer species. Moreover, we evaluated grazer activity on the different substrates during the experiment. The results support only the first hypothesis and indicate lower resource consumption on complex substrates compared with simpler substrates. Additionally, the effect of the grazing of the invasive species on taxon richness was greater in simplified than in complex habitats. The grazing activity on the substrate suggests a relationship between resource exploitation and habitat complexity in which the invasive grazing species visited the simple habitat less frequently. However, the effects of invasive grazers on food resources were higher on the simple substrate. The effects of grazing activity on food resources depend on the interaction between habitat complexity and grazer species. In this way, the introduction of an invasive species may have negative impacts on the structure and function of periphytic communities, mainly in simplified aquatic ecosystems.