Background: Understanding fish movements and migrations are paramount for management and conservation efforts. By applying Hidden Markov Models (HMMs) on records from electronic tags, migration routes of tagged fish can be reconstructed and new insights to the movement ecology of a species can be gained. We demonstrate the usability of HMMs on a widespread, iteroparous salmonid (sea trout, Salmo trutta) in a complex marine area with highly variable temperatures and salinities within small geographic distances. Understanding how the highly adaptable sea trout cope with these complex conditions could shed new light on factors driving the movement ecology of salmonids. Migration tracks of fish migrating at sea are reconstructed by applying an HMM on temperature and depth records from eight wild post-spawned sea trout from four Danish rivers. Results: The fish migrated at sea for 47-142 days. Estimated positions of all fish were close to the coast (<100 km) throughout the marine period, but migrations along coastlines up to 580 km away from the natal river occurred. Seven of eight individuals resided in or actively migrated into stratified or shallow marine areas that heat up fast during spring, while all eight individuals resided in deeper and more heterogeneous areas that heat up slow during summer. All fish entered the Skagerrak (located between Denmark and Norway) at some stage during summer. Migrations were directed into less saline areas during the first 15 days at sea for all individuals. Mean linear progression of the fish was 16 km day-1 (range 0-58 km day-1). Conclusions: The results corroborate the expectation that sea trout are more coastally orientated than other salmonids, but also suggest that longer migrations occur in the seas surrounding Denmark compared to elsewhere. This could be a consequence of the fish seeking out habitats with optimal conditions (e.g. salinity, temperature, predation and foraging options) for growth in different parts of the year. The coinciding movement from shallow or stratified marine areas that heat up fast during spring to deeper, more well-mixed areas that heat up slow during summer suggested that some habitat selection had occurred. These results shed new light on factors influencing marine migrations in salmonids and demonstrate how HMMs can expand our knowledge on behaviour and movement ecology of marine fishes.