Research in the field of groundwater treatment indicates the prospects for the development of its complex purification involving various morphological types of microorganisms, fixed on inert contact materials. It was indicated that at certain parameters of water quality (pH 6–7; Eh 50...200 mV, in the presence of dissolved carbon dioxide and at magnitudes of permanganate oxidation of up to 5 mg О 2 /dm 3 ), development of bacteria of genus Gallionella prevails in groundwater, and development of bacteria of genera Lepthothrix, Crenothrix prevails at pH values of 6.5–7.5; Eh=–200...300 mV and PО>5 mg О 2 /dm 3 . This provides a series of advantages in the use of the biochemical method over conventional physical and chemical methods, in particular, acceleration of the process of water purification from ferrite compounds. It was shown that much less attention was paid to modeling the kinetics of the processes of treatment of underground water in bioreactors than to conventional physical-chemical methods, for which modern mathematical models were developed. That is why the development of the direction of modeling the biochemical process of water purification from iron compounds is a relevant task. The mathematical model is represented by the Cauchy problem for a nonlinear system of differential equations in partial derivatives of the first order. The system of the Cauchy problem consists of five equations with five unknown functions, which describe the distribution the concentration of ferrum cations, bacteria and the matrix structures in two phases (movable and immobilized) both in space and time. When constructing the model, we used both technological (maximum contamination capacity (2.6 kg/m 3 ), boundary magnitude of the bacteria biomass in the matrix structures (9.5 g/m 3 ), maximum specific rate of their growth (0.17–0.18 h –1 ), saturation coefficient (0.65–0.7 g/m), flow rate in the range of 5–20 m/h), and design parameters (the height of contact load of a bioreactor – 1.3 m). In the considered model, the time of effective operation of a bioreactor depends on the concentrations of cations of Fe 2+ , which in natural waters can be in the range of 0.5–20 mg/dm 3 , the number of ferrobacteria (10 2 –10 4 kl/dm 3 ), as well as the water flow rate. The inverse influence of the characteristics of the process, in particular, the concentration of matrix structures in the inter-pore space, as well as characteristics of the medium with the help of coefficients of mass exchange and porosity, were taken into account. The model allows determining the optimum operation time of a bioreactor between washings