The comparative estimation microbiological and abiogenous kinetics of oxidising processes, as well as their contribution to transformation of structure of stable isotopes of iron 56Fe and 54Fe in low-temperature mineral ferruginous “ Marsial water” (Southern Kareliya) springs and in light- salt spring of Staraya Russa “ (Novgorod region) resort was carried out. In a series of modelling experiments influence of initial concentration of iron and an oxygen mode was investigated on speed of oxidizing processes and transformation of isotope structure generated iron oxide with use of samples of natural water in situ. Isotope structure Fe was defined in the mineral ferruginous springs which differed on a chemical compound of waters and genesis. The structure of the microorganisms participating in reactions of oxidising branch biogeochemical cycle of iron was established. The prevailing role of the microbiological (biogene) factor in differentiation of isotope structure of iron oxidized deposits was shown.