The emerging field of environmental DNA (eDNA) is transforming our approach to how we assess biological diversity and ecosystem function. eDNA is used to describe DNA shed from secretory processes such as the sloughing of skin, scales, mucus, eggs, sperm, blood, or defecation, and can be used to provide a record of a species presence. When combined with recent advancements in next-generation sequencing and bioinformatics, the diversity of organisms from environmental samples that contain mixtures of DNA signatures can be recovered. As such, eDNA metabarcoding can provide a wealth of information for studies of fish biodiversity, food web dynamics, diet analysis, and for environmental and invasive species monitoring. We here highlight a number of studies based on coastal ecosystems across Australia, thus focusing on the development and application of eDNA metabarcoding for studying fish biodiversity across spatial and temporal scales, as well as methods development around laboratory protocols and taxonomic assignments. We additionally highlight how these advances might be incorporated into existing or new marine monitoring programs.