Two replicate multi-mesh gill and trammel nets, each comprising five 30 m long panels made from different-sized mesh (38, 54, 70, 90 and 100 mm stretched mesh openings) were fished in a south-east Australian barrier estuary over seven nights to evaluate their potential as sampling gears for fishery-independent surveys of estuarine fish assemblages. There were no differences in composition and structure of assemblages, mean abundance, or diversity of catches between the two types of net. The composition and structure of catches differed between mesh sizes, with the panels made from 38 and 54 mm mesh retaining significantly more fish and species than the larger-sized meshes. The two smallest mesh sizes were important for capturing sub-adults and juveniles of some species. Based on a greater precision of catch per unit effort (CPUE) estimates, less sampling effort and greater ease of use, the multi-mesh gill net was a better sampling unit than the trammel net for assessments of estuarine fish populations.