Understanding benthic community ecological and morphological functions in Temperate Mesophotic Ecosystems (TME’s) is essential to develop robust conservation strategies for TME’s, particularly in a changing world. Autonomous Underwater Vehicle (AUV) technologies have become useful tools for assessing spatial and temporal trends and patterns on benthic communities worldwide. As sponge communities are dominant structure and habitat providers for many vertebrate and invertebrate species in TME’s, as well as critical ecological service providers in nutrient cycling and benthic-pelagic coupling, our study focuses on characterizing the distribution, diversity and functional morphology of sponge communities in Storm Bay, SE Tasmania. Using underwater imagery derived from an extensive survey of these rocky reefs by the IMOS AUV facility, we detected significant variation in sponge community distribution, diversity and abundance with depth and with location through the Bay. We also investigated how size and shape of dominant sponge assemblages vary with depth and location across this anthropogenic-impacted coastal ecosystem and hotspot for global warming. Our findings provide a baseline on which to monitor future ecosystem change against and an insight into the relative magnitude of natural vs anthropogenic impacts on an Australian TME, vital information for the protection of these unique habitats.