The total factor productivity of the Commonwealth Trawl Sector of the Southern and Eastern Scalefish and Shark Fishery is estimated for the period 1996–97 to 2008–09 using vessel-level data and a traditional approach that captures the production decisions of fishers. The paper develops a replicable methodology and calculates benchmark productivity estimates by which future estimates for other Commonwealth fisheries can be evaluated. Productivity estimates presented in this paper are based on vessel-level financial and catch data collected by ABARES in its annual survey of the fishery and the application of the Fisher index method. The analysis of trends in productivity offers important new information to decision-makers. Changes in the way in which fishers organise the transformation of inputs into outputs have a direct impact on firm-level economic performance. Changes in productivity at the vessel level illustrate the response of the fleet to policy settings in the fishery and, more broadly, to environmental factors. This is of particular value for fishery managers when they consider policy instruments—such as fish stocks, technology and fleet structure—that might affect the drivers of productivity growth in fisheries.