Facultative air-breathing fish can survive extended periods in hypoxic water due to their capacity for aerial respiration. The majority of studies on air breathing fish response to hypoxia have been experimental under forced hypoxia. How air-breathing fish respond to hypoxic conditions in-situ has received little attention. Using high frequency acoustic tracking of the facultative air-breathing Australian lungfish, Neoceratodus forsteri, we investigated how lungfish respond to hypoxic zones and periods of holomixus. Lungfish were tracked within a river impoundment using depth sensitive transmitters and 26 acoustic receivers, to locate fish positions in 3-dimensions. Three-dimensional kernel utilisation distribution models (3D-KUD) were developed to investigate lungfish space utilisation in the presence and absence of an oxycline. During stratified conditions, lungfish maintained a 3D-KUD above the oxycline, rarely venturing into hypoxic waters. During holomixis, lungfish 3D-KUD expanded to utilising a wider range of depths. Despite N. forsteri having physiological adaptations to cope with anoxic conditions, the presence of hypoxic zones and the species narrow depth preferences, reduced the total space utilised to < 8 % of the study area substratum. With increasing demand for new impoundments in many tropical regions, our study provides insight into how air-breathing fish species might respond to altered environmental conditions.