The use of the biological method is promising for treating underground waters from iron compounds. Iron bacteria used in the process are widely spread in weak acidic and neutral underground waters containing iron ions (II), dissolved carbon dioxide and minimum concentrations of oxygen. The relevant direction of present-day biotechnology is the use of iron bacteria for treating underground waters. The goal of this research is to compare the efficiency of using the biological method for treating underground iron containing weak acidic and neutral waters under different conditions. As the test-objects, Gallionella and Lepthotrix iron bacteria were used. The sedimentation of bio-minerals was obtained from the washout waters of the biological deironing station. Calcium soda was used as an additional source of inorganic carbon for bacteria. As a result of the studies it is established that the use of the non-reagent method gives the possibility to achieve only 80% efficiency in removing iron compounds while the use of sodium carbonate results in increasing efficiency up to 93%. To determine the contribution of biological purification of ground water from iron compounds, the bacteria were inhibited with the preparation of polyhexamethylene guanidine (PHMG) chloride. It was found that inhibition of Gallionella and Lepthotrix led to the reduction of 50% of the iron removal effect. The mechanism was developed of inhibiting the process of iron bacteria metabolism by PHMG (polyhexamethylene guanidine). The new technology of arranging a block-module station for treating underground waters is proposed.