The sooty grunter (Hephaestus fuliginosus) is an endemic freshwater species which is abundant in many rivers across the wet tropics region in Northern Australia. Despite its ecological, social and cultural importance, there is currently limited ecological knowledge of this species in terms of its habitat use and movements, which is required to provide detailed advice for establishing environmental flows. This study used radio and acoustic telemetry to examine the diel movement, meso-habitat use, and activity of sooty grunter in the Daly River system, Northern Territory. Analysis of 17 radio-tracked juveniles over a 10-day monitoring period found that juveniles had positive associations with riffle and run habitats both during the day and night, and tended to avoid pool habitats. Acoustic-tracking data from 16 sooty grunter over a 4-month period indicated strong site fidelity, with most fish using less than 2 km of the 34 km study reach. Within these areas, small-scale movements were undertaken at strikingly regular periodicity and activity was highest during the day. These findings indicate the importance of riffle and run habitats for this species. This information will contribute to better informed management of water resources in the Daly River and other northern Australian rivers.