The region of the Filchner Outflow System (FOS) in the southeastern Weddell Sea is characterized by intensive and complex interactions of different water masses. Dense Ice Shelf Water (ISW) emerging from beneath the ice shelf cavities on the continental shelf, meets Modified Warm Deep Water (MWDW) originating from the Antarctic Circumpolar Current at the sill of the Filchner Trough. These hydrographic features convert the FOS into an oceanographic key region, which may also show enhanced biological productivity and corresponding aggregations of marine top predators. In this context, six adult Weddell seals (Leptonychotes weddellii) were instrumented with CTD-combined satellite relay data loggers in austral summer 2014. By means of these long-term data loggers we aimed at investigating the influence of environmental conditions on the seals’ foraging behaviour throughout seasons, focussing on the local oceanographic features. Weddell seals performed pelagic and demersal dives, mainly on the continental shelf, where they presumably exploited the abundant bentho-pelagic fish fauna. Diurnal and seasonal variations in light availability affected foraging activities. MWDW was associated with increased foraging effort. However, we observed differences in movements and habitat use between two different groups of Weddell seals. Seals tagged in the pack ice of the FOS focussed their foraging activities to the western and, partly, eastern flank of the Filchner Trough, which coincides with inflow pathways of MWDW. In contrast, Weddell seals tagged on the coastal fast ice exhibited typical central-place foraging and utilized resources close to their colony. High foraging effort in MWDW and high utilization of areas associated with an inflow of MWDW raise questions on the underlying biological features. This emphasizes the importance of further interdisciplinary ecological investigations in the near future, as the FOS may soon be impacted by predicted climatic changes.