AbstractTo deeply understand various geodynamic processes, including volcanic activities and earthquakes, it is essential to extract detailed information about Earth materials, such as lithology and geofluid, from geophysical, petrological, and geochemical observations of Earth's interior. We developed a Bayesian probabilistic framework that can estimate the lithology and geofluid type (aqueous fluid or melt), geofluid amount (porosity), and parameters related to the fluid geometry (aspect ratio and critical fluid fraction related to connectivity) from P‐wave and S‐wave seismic velocities and electrical conductivity data obtained from geophysical tomography. By conducting synthetic inversion tests, we showed that methods based on a joint probability distribution, which simultaneously determines all parameters, sometimes fail to narrow the number of possible answers from 78 lithologies (e.g., basalt, granite, and eclogite) × two geofluid type (melt or aqueous fluid) candidate sets. This failure is derived directly from the difficult nature of inversion problems with relatively large data uncertainties. The proposed method uses a marginalization technique that first estimates lithology and geofluid type and then quantifies geofluid parameter values, which can narrow the probable lithology, geofluid type, and geofluid parameter sets in many cases. In addition, the computational cost of the proposed marginalization method is comparative to a former joint‐estimation method, which is theoretically identical to a previous heuristic method based on the least squares method. Therefore, the marginalization method is useful for geophysical data analyses that involve large amounts of observational data with relatively large uncertainties.