The role of geomorphic structure, referred to as physical heterogeneity, and its influence upon the colonization of habitat by macroinvertebrates was analysed in the peri-urban, Twin Streams Catchment, in West Auckland, New Zealand. Using a cross-scalar approach, 4 riffle-run assemblages were analysed in each of 2 River Styles (a confined, low sinuosity, gravel bed river and a partly confined, low sinuosity, bedrock, cobble, and gravel bed river). Each of these 8 locations comprised 2 distinct sampling areas; the upstream zone had a more heterogeneous river bed with a high diversity of physical features and flow, whilst the downstream area had a more homogeneous structure. Microhabitat features sampled at each site included streambed material, bank margins, fine grained organic debris, wood, and boulders. Habitat mosaics and their associated macroinvertebrate relationships followed a semi-predictable but interrupted pattern, supporting the view that river systems are a patchy discontinuum. Homogeneous zones were more frequently characterised by higher proportions of Trichoptera than heterogeneous zones, whilst heterogeneous zones were frequently characterised by Plecoptera and Ephemeroptera. Diversity was maximised when the species pools from heterogeneous and homogeneous sites were combined for any given site. Functional habitats influenced macroinvertebrate assemblages in non-linear and complex ways. Wood and organic debris habitats were associated with high diversity, abundance, and sensitive species whereas streambed habitat was usually associated with low diversity. A diverse range of physical zones that approximates the ’natural range of behaviour’ for the given type of stream was considered to provide a more effective platform for rehabilitation planning than emphasising heterogeneity of physical structure in its own right. The role of geomorphic structure, referred to as physical heterogeneity, and its influence upon the colonization of habitat by macroinvertebrates was analyzed in the peri-urban, Twin Streams Catchment, in West Auckland, New Zealand. Using a cross-scalar approach, 4 riffle -run assemblages were analyzed in each of 2 River Styles (a confined, low sinuosity, gravel bed river and a partly confined, low sinuosity, bedrock, cobble, and gravel bed river). Each of these 8 locations has 2 distinct sampling areas; the upstream zone had a more heterogeneous river bed with a high diversity of physical features and flow, whilst the downstream area had a more homogeneous structure. microhabitat features sampled at each site included streambed material, bank margins, fine grained organic debris, wood, and boulders. Habitat mosaics and their associated macroinvertebrate relationships followed a semi-predictable but interrupted pattern, supporting the view that river systems are a patchy discontin uum. Homogeneous zones were more frequently characterized by higher proportions of Trichoptera than heterogeneous zones, whilst heterogeneous zones were frequently characterized by Plecoptera and Ephemeroptera. Diversity was maximized when the species pools from heterogeneous and homogeneous sites were combined for any given site. Functional habitsats influenced A variety range of physical zones that approximates the ’natural range of behavior ’for the given type of stream was considered to provide a more effective platform for rehabilitation planning than emphasizing heterogeneity of physical structure in its own right.