The aim of the article is to compare two classifications systems of engineering-geological environment sustainability in terms of its permeability evaluated on the basis of permeability coefficient. The first evaluated classification assumes a permeable environment to be a positive characteristic in the engineering-geological assessment, while the other considers an impermeable environment as favourable. The four fine-grained soil materials were selected, as they had very similar, almost identical grains-size distribution, but different microstructure characterized by grains sphericity, angularity, and roughness. At the same time, the influence of changes in the density of soil materials (density index 10%, 30%, 60%, 90%) was analysed. Permeability coefficient was determined using six methods (empirical formulae, laboratory and microscopic analysis). The laboratory method falling head test (FHT) was taken as a reference test that reflected the actual water flow through the soil. It was found that with an increase in grain angularity and roughness (and a decrease in sphericity), the permeability coefficient was decreasing and this trend culminated along with gradual compaction. Moreover, the research shows that unsuitable methods may classify soil materials into wrong engineering-geological permeability classes, which may have negative consequences during engineering-geological or geotechnical assessment and cause subsequent problems in foundation engineering.