The structure and geodynamic history of the northern Barents–Kara continental margin, which had formed mostly by the latest Paleozoic, have been investigated using offshore geological and geophysical data and geological evidence from adjacent landmasses. In the context of the suggested model, the Saint Anna trough is interpreted as a boundary tectonic element between the Svalbard and Kara plates. Thus, the study focuses on a complex tectonic node with its structure having implications for the trough origin, as well as for the history of geodynamic relations among Arctic cratons and microplates. Trough structures of different ages in the area, including the northeastern East Barents trough and the St. Anna trough, appear to be a zone of triple or T-shaped junction. The reported reconstruction of the trough system history since the Middle Paleozoic shows that the St. Anna trough joined the East-Barents system in the Late Permian–Triassic to become its new segment extending the system to the north.