Habitat availability underpins the diversity and distribution of benthic marine communities. Sponges are significant structural components of seabeds; therefore, understanding sponge-community associations are important for the effective management of marine biodiversity. Invertebrate communities were quantified from 11 sponge species having distinct morphologies from Ningaloo Reef (tropical) and Rottnest Island (temperate), Western Australia. Communities from substrate adjacent to sponges were additionally sampled for comparisons to sponge-associated fauna. Gross and fine-scale morphological features of sponge host species were quantified to assess their effects on faunal abundance and diversity. A total of 3966 individuals from 125 taxa were extracted, showing low co-occurrences of taxa from both sponges and the surrounding substrate (Ningaloo 8.9%; Rottnest 11.2%). Four out of the 11 sponges supported higher fauna abundance compared to their surrounding substrate, including Haliclona sp. NTM148 (Ningaloo; 1.21 ± 0.54 N.cm−3, 60 × higher than substrate) and Monanchora clathrata (Rottnest; 2.87 ± 1.7 N.cm−3, 32 × higher than substrate). These communities were dominated by the barnacle Acastinae sp.4 (100%) and sedentary polychaete Spionidae sp. 1 (99%), respectively, highlighting strong host-specific associations. Sponge size (volume), % of internal space, minimum diameter of internal space, and gross morphological complexity were important at explaining variation in faunal assemblage, with larger sponges having more internal space of larger minimum canal diameter supporting higher community abundance. This study highlights the significance of large and long-lived sponges as sources of unique marine biodiversity that are yet to be discovered and the importance of sponge gardens for the conservation of cryptic marine biodiversity.