Australia’s commercial and recreational fisheries are annually valued at in excess of $2.5 and 2.6 billion but, despite their undeniable importance, very few economically important species are supported by appropriate stock assessments. Most species are characterised by severe shortfalls in much of the required basic data, driven by the low value of many stocks, the high cost of independent monitoring and the subsequent reliance on low-quality, fishery-dependent data. There is a clear need for accurate and rapid stock assessments in the current climate of competing commercial, recreational and conservation interests. This investment will validate the use of environmental DNA sampling to estimate populations of Murray Cod and Mulloway in New South Wales and compare its utility with fishery-dependant methods for assessing relative abundances across appropriate spatio-temporal scales in the wild.