Exotic willows (Salix spp.) are widespread riparian tree species of rivers in temperate Australia and New Zealand. Despite being considered as a weed of national significance, little is known about the habitat value of willows and the impact on aquatic biota of vegetation change following willow management programmes. Macroinvertebrate fauna in root habitats of willows and Phragmites australis habitats were examined in three central Victorian rivers to understand the effect of such littoral habitat changes on macroinvertebrates. Data were analysed using Partially Nested Factorial ANOVA with season, river and habitat as main effects. Habitat structure had a significant effect (P < 0.05) on macroinvertebrate community assemblage. However, effect of habitat was not consistent among seasons. The greatest community differences among habitats were observed during winter and least separation during autumn. Taxa responsible for community differences among habitats were also identified. Species richness and abundance did not show consistent variation among habitats over different rivers or seasons. This study provided some indication of the macroinvertebrate community changes that would take place in situations where riparian vegetation changes takes place from willows to P. australis.