The critically endangered spotted handfish (Brachionichthys hirsutus) is restricted to a limited number of locations in south-eastern Tasmania, Australia. As is often the case for rare species, conducting statistically adequate surveys for B. hirsutus can be costly and time consuming due to the low probability of encountering individuals. For the first time we used a highly efficient and rigorous Global Positioning System (GPS) parameterised underwater visual census (GUVC) to survey B. hirsutus abundance within all nine known local populations in the Derwent Estuary within one season. In addition, a benthic microhabitat assessment was conducted simultaneously using a GoPro® camera attached to diver to determine B. hirsutus microhabitat preferences. B. hirsutus local populations varied between sites, with densities ranging from 1.58 to 43.0 fishes per hectare. B. hirsutus demonstrates a strong preference for complex microhabitat features, such as depressions and ripple formations filled with biogenic substrates (e.g. shells) but avoids simple, low relief microhabitats (e.g. sand flats) and areas dominated by ephemeral, filamentous algae. Complex microhabitats may enable B. hirsutus to avoid predators, increase forage opportunities or provide higher quality spawning sites. This first wide-scale application of GUVC for B. hirsutus allowed us to survey a larger number of sites than previously possible to provide a robust reference point for future long-term monitoring.