Seismic interpretation of 13 lines has been conducted in the Hammerfest and Tromsø basin areas in the southwestern Barents Sea. Based on interpretations, a 3D Geomodel comprising 10 layers has been constructed. Depth conversion of the Geomodel was accomplished after building of the herein required velocity model. Paleobathymetric reconstruction was performed for 9 time intervals from Top Oxfordian/Late Jurassic until Intra Sotbakken/Base Pliocene utilizing SINTEF´s basin modeling tool SEMI Paleowater. The restoration method is based on the information about depositional geometries from seismic sequences combined with zero or near zero water depth indicators. The time intervals have been restored using the deep marine infill scenario. The reconstruction showed that the Early Cretaceous paleo-water depth was greatly influenced by the Late Jurassic-Early Cretaceous rifting episode that resulted in the formation of deep marine basins and structural highs. Differential subsidence during the Cretaceous led to more stable areas in the east and rapidly subsiding basins in the west of the study area. Compressional tectonics in the Early Paleogene resulted in the development of the Senja Ridge as a positive structure. From the Oligocene until the Miocene, a period of shallow marine conditions was restored in the Hammerfest and Tromsø basins. The transition to a passive continental margin and resulting thermal subsidence led to a new deepening in the Neogene.