The paper presents the results of modeling the weathering effect on the carbonaceous material of shungite rocks (shungites) in two experimental systems modeling the processes of leaching in water and acid solution. The evolution of the composition, structural characteristics and surface properties were analyzed by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), Raman spectroscopy and laser microscopy methods. The changes in the trace element and REE content of the shungites in the model experiments correspond to the leaching in an acidic oxidizing environment. We observed a decrease in REE content accompanied by an increase in the share of heavy REE, as well as a more explicit Eu negative anomaly for the shungites that have been modified in water and acid solution. The data reveal a reduction of the interlayer ordering and surface roughness of shungites during the leaching experiments. Shungites with a relatively high structural ordering are characterized by higher resistance to leaching.