The crustal structure and continental margin between southern Nares Strait and northern Baffin Bay were studied based on seismic refraction and gravity data acquired in 2010. We present the resulting P wave velocity, density and geological models of the crustal structure of a profile, which extends from the Greenlandic margin of the Nares Strait into the deep basin of central northern Baffin Bay. For the first time, the crustal structure of the continent-ocean transition of the very northern part of Baffin Bay could be imaged. We divide the profile into three parts: continental, thin oceanic, and transitional crust. On top of the three-layered continental crust, a low-velocity zone characterizes the lowermost layer of the three-layered Thule Supergroup underneath Steensby Basin. The 4.3–6.3 km thick oceanic crust in the southern part of the profile can be divided into a northern and southern section, more or less separated by a fracture zone. The oceanic crust adjacent to the continent-ocean transition is composed of 3 layers and characterized by oceanic layer 3 velocities of 6.7–7.3 km/s. Toward the south only two oceanic crustal layers are necessary to model the travel time curves. Here, the lower oceanic crust has lower seismic velocities (6.4–6.8 km/s) than in the north. Rather low velocities of 7.7 km/s characterize the upper mantle underneath the oceanic crust, which we interpret as an indication for the presence of upper mantle serpentinization. In the continent-ocean transition zone, the velocities are lower than in the adjacent continental and oceanic crustal units. There are no signs for massive magmatism or the existence of a transform margin in our study area.