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Abstract Harbour seals are top predators in the North Sea and regarded as sentinels for ecosystem health. A few hundred also occur in adjacent estuaries, such as the Elbe estuary, Germany. However, only little is known about how these animals use this dynamic tidally influenced habitat, which has been under high anthropogenic pressure for decades. In this context, nine harbour seals (Phoca vitulina) from the Elbe estuary were equipped with biotelemetry devices to track their movements over multiple months. Harbour seal movements were characterised by short trips (trip length outside pupping season for females: 9.0 ± 1.12 km, males: 7.0 ± 1.24 km) as well as small home ranges (median 50% home range for females: 16.3 km2, males: 36.1 km2) compared to harbour seals from marine regions. Within the estuary, the animals utilised the fairway, river branches and tributaries. During the pupping season in June and July, four seals showed strongly reduced trip lengths and durations, increased daily haul out durations as well as smaller home ranges. Even though a continuous exchange with harbour seals from the Wadden Sea likely occurs, most individuals in this study spent the entire deployment duration inside the estuary. This indicates that the Elbe estuary provides a suitable habitat for harbour seals, despite extensive anthropogenic usage, calling for further studies on the consequences of living in such an industrialised habitat.