Aims: This study examines the life and health of Captain Tobias Furneaux (1735–1781), Royal Navy officer and companion to Captain James Cook, as an early case study of ear, nose, and throat (ENT) disease during Australian maritime exploration. It aims to highlight how chronic ENT conditions affected leadership, communication, and survival at sea, and to contextualise these within the broader development of naval medicine. Methodology: Primary historical sources, including ship’s logs, medical journals, and surgeon George Forster’s 1777 expedition notes, were reviewed for descriptions of oral, auditory, and respiratory symptoms in Furneaux and his crew. These were interpreted in light of modern otolaryngologic understanding to infer likely diagnoses and environmental risk factors. Results: Furneaux endured recurrent “affections of the gums and throat,” ulceration, and progressive weakness of the mouth and pharynx—consistent with advanced scurvy and chronic infection. Episodes of deafness and sinus congestion were also recorded, likely exacerbated by prolonged exposure to salt air, humidity, and smoke. Crude interventions such as vinegar gargles, salt rinses, and fumigation represent early, empirical attempts at ENT treatment, predating microbial theory and the discovery of vitamin C. Conclusion: Captain Furneaux’s deteriorating health illustrates the high burden of ENT morbidity among 18th-century naval explorers and its impact on operational effectiveness. His experiences reflect the environmental and nutritional origins of many ENT conditions and underscore how the challenges of long-distance sea travel helped shape early concepts of preventive and surgical otolaryngology in Australia’s maritime history.