Habitat complexity is often used to explain the distribution of species in environments, yet the ability to predict outcomes of structural differences between habitats remains elusive. This stems from the difficulty and lack of consistency in measuring and quantifying habitat structure, making comparison between different habitats and systems problematic. For any measure of habitat structure to be useful it needs to be applicable to a range of habitats and have relevance to their associated fauna. We measured three differently-shaped macrophyte analogues with nine indices of habitat structure to determine which would best distinguish between their shape and relate to the abundance and rarefied species richness of their associated macroinvertebrate assemblages. These indices included the physical, whole-plant attributes of surface area (SA) and plant volume (PV), the interstitial space attributes of average space size and frequency (ISI), average refuge space from predation (Sp/Pr), and total refuge space (FFV), and the degree of surface convolution at a range of scales (i.e. the fractal dimension at four spatial scales: 7.5×, 5×, 2.5× and 1× magnification). We found a high degree of inter-correlation between the structural indices such that they could be organised into two suites: one group describing interstitial space and surface convolution at coarse scales, the other describing whole-plant attributes and surface convolution at fine scales. Two of these indices fell into both suites: the average refuge space from predation (Sp/Pr) and the fractal dimension at 5× magnification. These two measures were also strongly related to macroinvertebrate abundance and rarefied species richness, which points to their usefulness in quantifying habitat structure and illustrates that habitat structure depends not just on shape, but on the space associated with shape.