Understanding movement and habitat requirements of endangered species is critical to conservation management. We evaluate fine-scale acoustic telemetry to study breeding-related movement and habitat use of the endangered Mary River cod Maccullochella mariensis in a riverine environment and, in relation to key environmental variables, to inform management. Movement activity varied significantly in relation to water temperature and diel period, and spatial occupancy and habitat selection varied substantially in relation to the nesting behaviour of Mary River cod. Important nesting habitat included a large hollow log mid-channel and well-shaded logs and log jams adjacent to the river bank. Extrapolating this information to the general population was inhibited by relatively small sample sizes, due in part to the restricted spatial scale of the hydrophone arrays and longitudinal movements of tagged fish beyond the acoustic range of our array. Notwithstanding this, our results demonstrate that (1) fine-scale acoustic telemetry can quantify complex biological behaviours in riverine environments; (2) Mary River cod require specific environmental stimuli and habitat to support the reproductive cycle; and (3) changing environmental conditions may influence Mary River cod behaviour, and understanding this response is necessary for sustainable management. Findings from this study can inform future applications of this methodology in riverine environments and contribute to the development of management strategies and habitat restoration activities supporting the recovery of Mary River cod populations.