The rivers and estuaries of coastal Australia provide habitat for numerous fish communities comprising various ecologically and recreationally important fish species. With concerns over the impacts of external pressures, such as fishing, hypoxic conditions or toxic algal blooms, mitigation methods involving habitat and stock enhancement have grown in recent years. However, monitoring system health and quantifying the effect of enhancing fish habitat relies on baseline knowledge of the existing fish assemblage and its habitat usage. Traditional sampling methods such as netting and video observation are very useful, but are also sometimes inhibited in rivers by local conditions, including complex cover (branches or man-made objects) or visibility (turbidity or tannins). High-frequency imaging sonar has recently expanded from monitoring subsea structures to fine-scale mapping of seafloor habitats and assessing the number, size distribution and behaviour of fish. To complement current surveys into the health of the Swan Canning Estuary, Western Australia, towed sidescan imagery of the riverbed was conducted to define patches of topographic complexity, due mostly to changing river banks and submerged structures. At various sites of differing habitat (sand flats, centre of the river, sheer river bank, complex structure) within the Upper Swan Estuary, the imaging sonar was positioned 1 m above the riverbed, recording passing/surrounding fish for 45-minute periods. Sonar fish targets of different size classes were counted to investigate the length distribution and numbers within size classes, across the different habitats. This presentation will focus on the performance of the sonar and the differences in numbers and size classes of fish observed between the habitat types.