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The weathering process has generally been considered from only a chemical/physical point of view, however recent observations of bacteria in weathered rocks have, led to questions about the importance of microbial activity. In order to examine this, an outdoor natural experiment has been performed in which an andesite rocky hill was immersed in running ground water at outside temperature for one year. The ground water is harvested from a depth of 150m for the establishment of the systems. The system was constructed in Kakuma Campus, Kanazawa University on April 2007, having the foot baths heated at 37℃ with disinfectant and the rocky hill with running natural ground water without any chemical and heating treatments. After 3 months of incubation in the footbath, biomineralization of carbonate minerals (calcite and aragonite) by Cyanobacteria was found. On the other hand, after one year, clay minerals (Smectite) and zeolite (Heulandite and Clinoptilolite) were found in only the rocky hill under natural conditions. Various kinds of microorganisms, such as Cyanobacteria, diatoms and bacteria accelerated weathering reactions of andesite (Tomuro-ishi) for building materials eroded on the surface, and to produce secondary minerals of bio-clays and zeolites. The microorganisms carry an important role to change water quality within such a short period. Large crystals of zeolite and fine thin films of smectite attached to the microorganisms with cohesion organics to form green microbial mats on the surface of the andesite rocky hill, showing accumulation of elements such as Al and Si which could have been derived by dissolution of the rocks associated with running water. These data collectively demonstrate the microbial formation of smectite and zeolite of bio-clays, where the reaction rates may be substantially enhanced by the presence of microorganisms. Bacteria and diatom activity may hence have a great influence on the clay mineral developments commonly observed in naturally weathered rocks. The mechanism of bio-clays formation has important implications for water-rock interactions both in natural environments and in polluted areas. The footbath facilities will be made available for use not only in research, but also for the advancement of education while contributing to the local community.