Willows (Salix spp.) are an abundant alien tree and have been the mainstay of river bank protection throughout New Zealand. Riprap is another method of bank stabilisation consisting of rocks used to amour shorelines to protect against erosion. There is a trend for increasing use of riprap to replace willow along the banks of large rivers in New Zealand, but there is limited information on the ecological roles of these different bank types to support management. The objectives of this research were to determine the effects of different bank habitats on nearshore fish and invertebrate communities in the Waikato River as it passes through Hamilton city. The study involves three sites situated along the river. Each site has four bank types consisting of willow, riprap, a mixture of willow and riprap, and beach. Invertebrate sampling was carried out on three occasions to assess if there was a seasonal effect on community composition. Fish were sampled bimonthly determine differences in community composition. Assessment of fish populations was carried out with using boat electrofishing, Gee minnow trapping and spotlighting, while invertebrate populations were sampled by kick netting. Few significant differences were detected in invertebrate diversity between willow, riprap and willow/riprap habitats. However, community composition based on relative abundance was different among contrasting habitats in most seasons and Pielou’s evenness was greater for the more homogenous beach and riprap habitats. Riprap had consistently high alpha diversity but had lower species accumulation on two out of three dates suggesting there was a limited pool of taxa colonising the riprap compared to other habitats. Pairwise dissimilarity coefficients and PERMANOVA comparisons indicated that, although low in alpha diversity, beach habitats contributed significantly to macroinvertebrate beta diversity, and that willow and riprap habitats also supported different combinations of taxa due to different physical conditions. The combination of beach and willow habitats gave the highest gamma diversity. Willow habitats supported the highest number of both introduced and native fish, mainly reflecting abundances of common smelt, likely due to provision of cover, complex aquatic habitat, and riparian vegetation supplying detritus and invertebrate food resources. Riprap habitats supported the highest number of common bully. Common bully were also significantly larger in this habitat. Variations in water temperature, amount of shade, and river levels were possible factors contributing to temporal influences on biological patterns. The findings of this study indicate that, if all banks habitats in Hamilton City were composed of a single type, invertebrate biodiversity would be reduced. While the combination of beach and willow habitats may sustain high diversity for invertebrates and fish, the novel habitat provided by riprap may also favour some native fish and invertebrates over others. Therefore, a balance of different bank habitat types would perhaps be best to sustain present-day biodiversity levels in near shore macroinvertebrate and fish communities.