Snapper (Chrysophrys auratus) is an important commercial and recreational species, in Australia and New Zealand. From late winter to early summer, adult snapper migrate the broader metropolitan waters of Perth Western Australia into the protected embayment’s of Cockburn Sound, Warnbro Sound and Owen Anchorage to form spawning aggregations. In Cockburn Sound, they can be acutely exposed to anthropogenic (e.g. industry, fishing) and environmental factors (e.g. deoxygenation, elevated temperatures) that may affect numbers, spawning success and subsequent recruitment. Monitoring the status of these tightly-managed aggregations is particularly important as impacts of these stressors can be significant and rapid. To facilitate this monitoring, evaluation of commonly used methods for estimating spawning biomass (e.g. daily egg production method), against those that take advantage of developing methods (e.g. hydroacoustic), would be beneficial. To this end, active-acoustic data were collected from spawning aggregations of snapper in Cockburn Sound over two days in November 2016 to determine the packing density, vertical and horizontal distribution and length estimates of individuals (using a BioSonics DT-X single-beam echosounder at 38 and 120 kHz and a BlueView M900-2250 multibeam echosounder at 900 kHz). Length estimates were compared with historic fishery-independent length data. Acoustic data were analysed using Echoview software. Computed tomography scans of individual snapper were used to model the frequency-dependent acoustic backscatter and validate the BioSonics information from single targets. We approximated school shape and packing density using novel model approaches which can deliver estimates of school biomass, with accompanying error estimates. This study forms the first step towards an acoustic assessment of snapper in Cockburn Sound, which could be applied to other aggregations in Western Australia and elsewhere across its distribution.