Abstract
Monitoring cetaceans in Australia's Great Barrier Reef (GBR) is essential for understanding their ecological roles and informing conservation, yet traditional visual surveys are limited by logistical constraints. Passive acoustic monitoring (PAM) offers a complementary solution, particularly in acoustically complex coral‐reef habitats of the southern GBR. Over 2 years, we deployed an autonomous recorder at Lady Elliot Island to document cetacean presence and assess environmental associations. We detected vocalizations from humpback whales ( Megaptera novaeangliae ), dwarf minke whales ( Balaenoptera acutorostrata subsp.), and delphinids, likely spinner ( Stenella longirostris ) and/or bottlenose dolphins ( Tursiops spp.). Humpback whale song dominated recordings from June through October, while dwarf minke whale “Star‐Wars” calls occurred from May to August, marking the first acoustic evidence of this subspecies within the southern GBR. Dwarf minke whale detections correlated positively with chlorophyll‐ a concentration, whereas humpback whale detections were negatively associated with wind speed. Rorqual vocalizations declined during periods of elevated anthropogenic noise, while odontocete detections remained unaffected. These results highlight PAM's effectiveness for detecting cetaceans within complex reef soundscapes and suggest acoustic niche partitioning among taxa. These critical baseline data inform management strategies for understudied GBR cetacean populations and establish a robust framework for future long‐term monitoring efforts and effective conservation actions.