Improved knowledge of habitat use and movements is needed to support recovery of threatened riverine fish species. The trout cod (Maccullochella macquariensis) is a nationally threatened fish species endemic to rivers of the southern Murray–Darling Basin (MDB), Australia. This study investigated diurnal and nocturnal habitat use and movements of trout cod in the Goulburn River, using radio-telemetry. Trout cod typically occupied small reaches (<300 m) of stream during the late spring–summer study period. Larger-scale movements (mostly home-range shifts) and movements onto inundated riparian habitats also occurred during a period of high discharge. Trout cod occupied deeper water further from the bank during the day and shallower water closer to the bank during the night and used areas with slower velocities more than was their availability, particularly during the earlier hours of the day. They also made extensive use of in-stream cover (i.e. wood). Our information on diel habitat use provides a platform to guide informed management (e.g. availability of preferred habitats under different river-discharge scenarios) to improve trout cod population sustainability.