Broad-scale anthropogenic disturbances that reduce the density of epifauna and homogenise surficial sediments can have important consequences for seafloor biodiversity. We investigated the habitat structure and macrofaunal diversity of relatively simple soft-sediment habitats over a number of spatial scales (cm to km) to identify the role of habitat structure in influencing macrobenthic diversity and to assess the validity of using habitat structure as a surrogate measure for biodiversity. We sampled 10 locations with differences in habitat structure using a sampling design that nested macrobenthic core samples within videoed transects of the seafloor. This allowed us to determine relationships between observable habitat structure and macrobenthic diversity at a number of spatial scales. We characterised elements of habitat structure based on direct counts of surficial sediment characteristics and the presence of other immobile features, many of which were biogenic in origin. We also used multivariate measures (the relative multivariate dispersion, the mean and range of the Bray-Curtis dissimilarity along the transects) to characterise habitat structure at the transect scale. We developed regression models based on measures of habitat structure that explained 74 to 86% of the variance in macrobenthic diversity. This result suggests that removal of habitat structure in relatively low-structure soft-sediment systems will significantly decrease their biodiversity, and consequently that of the wider marine ecosystem.