The general features of ecological-geological systems (EGS) of rock massifs are determined as objects of geoecological research and engineering and environmental surveys. Ecological and geological systems include abiotic (lithotope, edaphotope) and biotic (microbocenosis, phytocenosis, zoocenosis) components. The characteristic features of the ecological and geological systems of natural rock masses are revealed on the example of the EGS of cemented carbonate and chalk soils and their weathering zones in the Southern Urals, Crimea, Belgorod region, Altai and Sikhote-Alin. On the example of karst caves in the Southern Urals, a characteristic is given of the geological processes of carbonate soil massifs and their microbial communities. The geological features of the development of soil covers on massifs of rocky cemented carbonate soils of the Crimea are described. The features of arthropod habitation on the Cretaceous rock massifs of the Belgorod region are revealed. Using the example of the Sikhote-Alin volcanic belt (rhyolitic tuffs) and the Teletskaya fault zone (silty-argillaceous formations of weathered gneisses and shales), the importance of biomineral complexes in the life of ungulates is shown.