Submarine canyons increase seascape diversity on continental margins and harbour diverse and abundant biota vulnerable to fishing. Because many canyons are fished, there is an increasing emphasis on including them in conservation areas on continental margins. Here we report on sponge diversity and bottom cover in three canyons of South-eastern Australia, test the performance of biological and abiotic surrogates, and evaluate how biological data from detailed seabed surveys can be used in conservation planning in these habitats. The biological data on sponge assemblage structure and species richness were obtained from 576 seafloor images taken between 148 and 472 m depth, yielding 65 morphospecies. Seafloor characteristics were similar within and between canyons, being almost exclusively composed of sediments with very few rocky substrates of higher relief. This environmental homogeneity did not, however, translate into biological uniformity of the megabenthos, and environmental factors were consequently poor predictors of biological features. By contrast, total bottom cover of sponges was highly correlated with species richness and served as a good proxy for species-level data in this situation. Design strategies that employ information on cover or richness of sponges provided a large dividend in conservation effort by dramatically reducing the number of spatial units required to achieve a specified conservation target of 50–90% of species to be included in reserves. This demonstrates that image-derived data are useful for the design of reserves in the deep sea, particularly where extractive sampling is not warranted. Using biological data on the sponge megabenthos to identify conservation units can also minimise socio-economic costs to fisheries because of a smaller geographic and bathymetric ambit of conservation areas.