This article presents a novel methodology for data integration including laboratory data, the results of standard well logging measurements and interpretation and the interpretation of XRMI imager data for determination of the porosity and permeability of the fracture system in carbonate rock. An example of the results of the micro computed tomography applied for carbonate rock is included. Data were obtained on the area of the Polish Lowland Zechstein Main Dolomite formation. The input set of data included the results of mercury injection porosimetry (MICP), thin section and polished section analysis, well logging measurements and comprehensive interpretation and micro computed tomography. The methodology of the macrofractures’ analysis based on borehole wall imagery as well as estimation of their aperture was described in detail. The petrophysical characteristics of the fracture systems were analyzed as an element of standard interpretation of well logging data along a carbonate formation. The results of permeability determination, with micro-, mezzo- and macrofractures’ presence in the rock taken into consideration, were compared with outcomes of the drill stem tests (DSTs).