Bank stabilization is increasing along large rivers as urban areas expand, and the need to protect infrastructure increases in the face of changing climate and flow patterns, but the cumulative effects of different stabilization approaches on reach‐scale biodiversity are not well understood. We investigated physical habitat characteristics and macroinvertebrate community composition and diversity for four shore‐zone habitat types across nested spatial scales over two sampling occasions. Distinct physical conditions were evident for riprap, beach and willow (mixed trees dominated by Salix spp.) habitats, reflecting variations in the combinations of shade, water velocity and substrate size/type, but there was wide variation in habitat conditions for mixed willow‐riprap sites. Additive biodiversity partitioning decomposed reach (γ) diversity into within (α) and among (β1) sample, among habitat (β2), and among site (β3) components, and highlighted significant effects of all spatial scales on macroinvertebrate diversity. Low autumn water levels led to truncated species accumulation curves at beach sites where macrophyte beds that supported macroinvertebrates became stranded, or elevated species accumulation curves for exposed willow‐riprap sites where the river benthos was sampled during hydrological disconnection of bank habitats. Spring and autumn differences in macroinvertebrate community composition were stronger than differences between habitat types. Our findings (a) highlight the interacting effect of river level with shore‐zone habitat function, and (b) underscore the importance of maintaining a diversity of bank habitat types at multiple sites along river shore‐zones to maximize macroinvertebrate diversity.