Human activities have pervaded aquatic ecosystems worldwide. As a result, riparian zones (the areas adjacent to rivers and streams) display high proportions of non-native vegetation, which is often considered symbolic of degradation and poor river health. Research suggests that riparian vegetation is essential for maintaining river health. However, whether this is due to the relative effect of vegetation species composition (including non-native vegetation) or vegetation structure (attributes such as canopy cover and linear continuity) is unclear. We used a comprehensive, regional ecosystem-health monitoring dataset to determine the effects of riparian vegetation across several spatial scales on river health and macroinvertebrate community composition. Constrained ordination methods revealed that riparian vegetation structure at the site scale influenced macroinvertebrate assemblages. However, when explicitly assessing the effect of non-native vegetation at the site scale, the proportion of non-native vegetation in the canopy did not influence macroinvertebrate assemblages. Notably, when species composition including both native and non-native species was assessed across all strata (canopy, shrub, and ground), it was found to significantly influence macroinvertebrate assemblages. This is likely driven by the different structural attributes of the various riparian vegetation communities found throughout the region. Therefore, the dominant effect of riparian vegetation structure may reflect the impact of different land uses within the area, rather than a strong influence of vegetation species identity on instream condition. These findings have important implications for riparian restoration. Our results suggest that the common restoration practice of focusing on non-native riparian vegetation removal combined with small-scale native replanting may not improve water quality and macroinvertebrate diversity, particularly where vegetation structure is modified in the process.