The NSW Estuarine Asset Protection program (NEAP) was established in response to the devastating 2022-2023 floods on Australia’s east coast. It aimed to establish a contemporary biodiversity baseline for estuaries in New South Wales (NSW), in close collaboration with local and state government departments as well as 13 indigenous groups. The program conducted extensive environmental DNA metabarcoding (eDNA) surveys and conventional surveys (BRUV + electrofishing) to characterise estuarine species assemblages at a state-wide scale. We collected 3,762 eDNA samples from 182 sites in 41 estuaries, with 581 fish species detected to date. This talk will explore the multiple uses of this contemporary baseline. Research and applications include assessing the impacts of the Tropical Cyclone Alfred induced flood events in 2025, effects of seascape patterns on fish assemblages, biogeography of elasmobranchs, spread of invasive pest species, and comparisons with conventional survey methods. The new baseline shows how novel monitoring approaches can improve our ecological understanding of estuarine fishes on a macroecological scale, while offering practical insights to management bodies in assessing changes in estuarine health.