Human-induced global climate change is documented to be increasing frequency and severity of weather events, resulting in impacts in aquatic environments. Recently, Australia experienced three successive phases in La Niña (2020-2023), leading to record breaking, persistent, rainfall across eastern Australia. Preceding the prolonged La Niña and more locally, the east Gippsland catchment, Victoria, experienced significant bushfires that burnt ~56% of the catchment. Gippsland Lakes, the catchment’s watershed, experienced complex environmental changes. The system hosts a resident population of Burrunan dolphins (Tursiops australis). In 2020, dolphins were observed with ulcerative lesions, reported as freshwater skin disease, with photographic data demonstrating a significant increase in lesion prevalence affecting ~90% of the captured population, leading to a mortality event. This event saw 25 confirmed and/or presumed deaths. Between 2020-2023, 124 surveys were conducted, with 170,708 images processed following standard dorsal fin-identification. Coupled with our 10-year population and seasonal sightings database, we assessed the full extent of the mortality event. Post-mortality event dolphin identification show only ~30 resident individuals remain, thus a ~60% decline in the already critically endangered population. Together with recent evidence of globally high levels of toxicants, there is growing concern about the population’s viability and risk of localised extinction