BackgroundFor diving, marine predators, accelerometer and magnetometer data provides critical information on sub-surface foraging behaviours that cannot be identified from location or time-depth data. By measuring head movement and body orientation, accelerometers and magnetometers can help identify broad shifts in foraging movements, fine-scale habitat use and energy expenditure of terrestrial and marine species. Here, we use accelerometer and magnetometer data from tagged Australian sea lions and provide a new method to identify key benthic foraging areas. As Australian sea lions are listed as endangered by the IUCN and Australian legislation, identifying key areas for the species is vital to support targeted management of populations.MethodsFirstly, tri-axial magnetometer and accelerometer data from adult female Australian sea lions is used in conjunction with GPS and dive data to dead-reckon their three-dimensional foraging paths. We then isolate all benthic phases from their foraging trips and calculate a range of dive metrics to characterise their bottom usage. Finally, k-means cluster analysis is used to identify core benthic areas utilised by sea lions. Backwards stepwise regressions are then iteratively performed to identify the most parsimonious model for describing bottom usage and its included predictor variables.ResultsOur results show distinct spatial partitioning in benthic habitat-use by Australian sea lions. This method has also identified individual differences in benthic habitat-use. Here, the application of high-resolution magnetometer/accelerometer data has helped reveal the tortuous foraging movements Australian sea lions use to exploit key benthic marine habitats and features.ConclusionsThis study has illustrated how magnetometer and accelerometer data can provide a fine-scale description of the underwater movement of diving species, beyond GPS and depth data alone, For endangered species like Australian sea lions, management of populations must be spatially targeted. Here, this method demonstrates a fine-scale analysis of benthic habitat-use which can help identify key areas for both marine and terrestrial species. Future integration of this method with concurrent habitat and prey data would further augment its power as a tool for understanding the foraging behaviours of species.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40462-023-00386-1.