As we know, the main goal of interpreting the materials of well logging, including the allocation of collectors and assessment of their saturation, are successfully achieved when the process of interpretation has a strong methodological support. This means, that it is justified by the necessary interpretational models and effective instructional techniques are used. They are based on structural and petrophysical models of reservoirs of the section investigated. The problem of studying the marl rocks with the help of the geophysical methods is not worked out properly. Many years of experience of studying limestone and marl rocks has made it possible to justify the optimal method of data interpretation of geophysical research wells in carbonate sections, which was represented by limestone and marl formations. A new method was developed to study marl rocks. It includes the following main studies: detection of reservoirs in the carbonate section according to the materials of geophysical studies of wells; determination of the geophysical parameters of each reservoir; assessment of the quality of well logging curves; introduction of amendments; selection of reference layers; the calculation of the relative double differencing parameters; the involvement of core data; identifying the lithological rock composition; the rationale for structural models of reservoirs; the definition of the block and of the total porosity; determination of argillaceous carbonate rocks; determination of the coefficient of water saturation of formations based on the type of the collector; setting a critical value for effective porosity, etc. This method was applied in the Eocene deposits of the Interfluve of the Kura and Iori, which is a promising object of hydrocarbons in Azerbaijan. The following conclusions have been made: this methodology successfully solves the problem of petrophysical characteristics of marl rocks; bad connection is observed between some of the reservoir parameters and permeability of the Eocene rocks in the Interfluve of the Kura and Iori; the presence of marl rocks in this region complicates the structural model; testing leads to deterioration of the filtration properties of reservoirs etc.