The Sustainable Rivers Audit (SRA) is an annual assessment of river health implemented by the Murray Darling Basin Commission.  The SRA framework is designed to assess river health at three broad geographic scales, the Basin, the watershed and sub-watershed ‘process’ zones.  A pilot study using various themes including fish was carried out in 2003 to ensure the SRA provided an effective and cost efficient assessment of river health. This paper compares river health assessments at regional scales using combinations of electrofishing, fyke net, and bait trap data and evaluates whether to include fish that were observed but not handled. 13,952 fish from 27 species were collected across the 92 sites with a further 9974 fish observed only. Analyses include individual metrics comparisons but we focus on community data and regional health assessments. Occasionally electrofishing missed a species at watershed and sub-watershed scales but electrofishing at the watershed scale averaged 92% similarity to the all methods data. River health assessments were not compromised if metric reference conditions (e.g. Maximum species richness lines) were adjusted accordingly. Electrofishing, when supplemented by bait traps, significantly reduced the cost of the fish-sampling program and is currently used in the fish component of the SRA.