The accurate interpretation of well-logging data is a crucial stage in the exploration of gas- and oil-bearing reservoirs. Geological formations, such as the Miocene deposits, present many challenges related to thin layers, whose thickness is often less than the measurement resolution. This research emphasizes the potential of utilizing electrofacies in such challenging environments. The application of electrofacies not only allows for the grouping of intervals with similar physical characteristics but can also be useful for estimating porosity and permeability parameters. For this purpose, various clustering methods were tested, including the 2D indexed and probabilized self-organizing map (IPSOM) method with and without supervision. Subsequently, the usefulness of the obtained results to improve the estimation of porosity and permeability parameters with the help of artificial neural networks was verified. As a result of the conducted analyses, significantly better results were obtained compared to classical petrophysical interpretation. The calculated porosity and permeability parameters were characterized by much greater variability and alignment with laboratory measurements on porosity and permeability. The best results were obtained for the IPSOM method, but the other methods did not differ significantly. In conclusion, the studies have shown a positive result of applying clustering methods, including the IPSOM method, to improve the estimation of permeability and porosity parameters in complicated, thinly-layered formations.