Many estuaries are important nurseries for various elasmobranchs, but conventional survey methods can fail to document species at low density. Environmental DNA (eDNA) methods do not require direct observations and are effective at detecting low-abundance taxa, making them ideal to record cryptic species and for community-level assessment at scale. Using a multi-year (2024–2026) eDNA dataset from 39 estuaries along the New South Wales coast, we characterised estuarine elasmobranch communities, environmental drivers, and response to an extreme flood event linked to a tropical cyclone. We detected 47 taxa across the 39 estuaries, including nine threatened species, ranging from single detections of IUCN Red List Critically Endangered giant guitarfish (Glaucostegus typus) and grey nurse sharks (Carcharias taurus) to the Vulnerable estuary stingray (Dasyatis fluviorum), present in 77% of estuaries across all seasons. We revealed a 115-km poleward range extension for the estuary stingray, consistent with the rapid warming of Australia's east coast. Community composition was structured primarily by latitude, temperature, and salinity, and estuary zone (upper, middle, lower) shaped within-system patterns. Bull sharks (Carcharhinus leucas) were distinct summer, upper-estuary indicators, while common stingaree (Trygonoptera testacea) was a significant indicator of the lower and middle estuary zones. Eleven estuaries sampled before and after Tropical Cyclone Alfred (March 2025) showed community disruption, where mean species richness fell from 6.1 to 4.1 as salinity dropped from 25 to 8 ppt. Detections of threatened species, including the Australian bull ray (Myliobatis australis), were lost from previously occupied systems, and recovery trajectories were governed by zone, salinity, and dissolved-oxygen gradients rather than time since disturbance, with lower zones rebounding fastest. Together these findings demonstrate the power of eDNA surveys to monitor mobile, threatened taxa, detect range shifts, and capture community responses to acute climate-driven disturbance, offering a scalable tool for estuarine conservation under increasing environmental pressure.