A vast range of methods are applied to measure marine biodiversity to provide critical scientific data for environmental management. In recent years, environmental DNA (eDNA) has emerged as a powerful tool for biodiversity assessment, offering a non-invasive and efficient method for detection and monitoring species from across the tree of life. In this project, we evaluated eDNA monitoring approaches in offshore marine surveys, focussing on relatively well characterised fish fauna. eDNA samples were collected throughout the water column, via CTD Niskin bottles and filtering as well as via a passive eDNA sampler, aboard the RV Investigator at sites from Tasmania to NSW, including sites within the South-East Marine Park Network, to establish a new baseline and provide a unique eDNA-based perspective on biodiversity in the south-east marine region. The eDNA data generated by the different water filtering protocols were compared spatially (between sites and depths). Biodiversity data was also collected in parallel using a suite of conventional methods (i.e trawl nets and deep towed-cameras) allowing direct comparisons to be made between eDNA methods and traditional surveying approaches. The evaluation of different eDNA sampling methods will provide guidance for designing effective and scalable bio-monitoring tools for Australian marine ecosystems.