The bathymetry is the most superficial layer of the Earth’s crust on which it is possible to perform direct measurements. However, it is also well known that water covers more than 70% of the Earth’s surface, so an enormous expenditure of acquisition campaigns should be performed to produce a high-resolution map of this layer. Currently exploiting mainly commercial navigation routes, the sea floor coverage with shipborne sounding is only at 11%, and the remaining part is currently modeled by classical interpolation techniques or satellite-based gravity inversion methods. In the present work, a new method to refine bathymetry modeling based on the exploitation of global gravity field models is presented. In the proposed solution, once modeled and removed from the observed gravity field, the gravitational signals related to the deepest structures, a 3D Bayesian inversion algorithm is used to improve the actual knowledge of bathymetry. The proposed inversion method also enables limiting the solution to shipborne sounding measurements in such a way as to improve the seafloor grid where no local, high-quality information is available. Two test cases are discussed in the Mediterranean Sea region. Promising results are presented, opening the possibility of applying an analogous method to refine the bathymetry modeling at larger scales up to the global one.