Sea turtles migrate between nesting beaches and foraging grounds, but little is known about the cues they use to direct these migrations, and the habitats that define their foraging grounds. Here, we used satellite telemetry to follow the movements of 11 flatback turtles Natator depressus after nesting on islands in the waters off the coast of the Kimberley region of northern Australia. State-space models were used to objectively define inter-nesting, migration and foraging behaviour during the 327 ± 315 d (mean ± SD) that the turtles were tracked. These animals migrated along the coast in water depths of 63 ± 5 m to foraging grounds on the mid-Sahul Shelf in the Timor Sea in average water depths of 74 ± 12 m, 135 ± 35 km from shore. Distribution modelling showed that flatback turtles preferred foraging and transiting in clear waters (suspended material <0.06 g m−3), 60 to 90 m deep and in association with complex, benthic geomorphology (banks, shoals, terraces, deep holes and valleys) thought to support a high abundance of sessile invertebrates, the likely targets of their foraging. Distance to the tidal front was also a strong predictor of turtle migratory behaviour, with the animals potentially following tidal fronts along the Kimberley coast. Our study identified both critical habitats for this species and the environmental variables that predict their migration and foraging. This information is important to aid spatial planning of conservation for this data-deficient species that is endemic to northern Australia.