The possibilities of the joint inversion of the modern multi-type geophysical (3D seismic, gravity & magnetic and electromagnetic) and geochemical data sets are demonstrated for the purposes of the oil-andgas-bearing capacity estimation and geological risk assessment in the sea shelf areas where no well logging information and other priory constraints are available. Methods, algorithms and software are developed for the construction of the coordinated 3D models of the media physical properties. The utilisation of the density model (as obtained from gravity data) as the low-frequency model for seismic inversion is suggested and demonstrated. It is shown that the joint inversion of seismic and magnetic data helps to authentically differentiate between carbonate reef and buried volcano structures. The regular links are ascertained between bottom sediments hydrocarbon gases concentration and structural and tectonic characteristics of the sub-surface that become apparent in seismic attributes. The method for the qualitative estimation of the hydrocarbon reservoir depth is developed based on the modelling of the gases filtration from reservoir to the surface. The principles are suggested for the recognition and prospectivity estimation of the oil and gas complexes from the joint analysis of the different data types.