Biological invasions are one of the main factors responsible for the imperiled status of freshwater ecosystems, but much remains to be learned about their indirect effects on native communities. The first part of this dissertation examines community effects of long-term efforts to selectively control invasive Eurasian watermilfoil. Results of the first study show that native plants immediately recolonized treated areas and habitat complexity was unaffected. Fish community was not influenced by invasive plant control. Macroinvertebrate communities were highly variable and part of their variability could be explained by plant community attributes. Both fish and macroinvertebrates used invasive watermilfoil, which emphasizes the need for timely restoration of native macrophytes to mitigate for lost habitat. Because fish and macroinvertebrates were more affected by complexity than other attributes of plant assemblage, reestablishment of habitat complexity appears to be a promising restoration strategy. The second study, which examined species interactions after watermilfoil control, found that fish feeding activity was not correlated with invasive plants or habitat complexity and that invasive macrophyte control did not affect characteristics of fish feeding investigated. The relationship between fish and macrophytes was further explored in the context of interactions between an invasive piscivore and its native prey. First, I examined the prey naiveté hypothesis with non-native peacock bass in Paraná River, Brazil. Prey responded to visual and chemical cues of peacock bass and displayed avoidance behaviors similar to those observed with a native predator, meaning that lack of recognition was not responsible for the observed vulnerability of native species to this introduced predator. After confirming lack of naiveté, I assessed direct and indirect effects of this non-native predator on native prey. Peacock bass had no indirect effects on its prey feeding activity. Macrophyte type did not affect indirect predator-prey interactions, whereas direct predator effects slightly decreased in the presence of aquatic vegetation. I discuss implications of these findings for native biodiversity and convene other potential explanations for the observed effects of peacock bass. Both projects contribute to our understanding of the relationship between aquatic plants and their animal communities and effects of invasive species in freshwater habitats.