The aim of this research was to determine the effectiveness of iron and manganese removal from groundwater using chalcedonite sand as a filter bed in rapid filtration. The experiment was conducted at a pilot plant. At the first stage of research, chalcedonite and silica sand were compared. The ripening time for manganese removal of chalcedonite was 27 days while silica sand was ripened within 57 days. At the second stage of research, the filtration process was conducted through chalcedonite sand with the rate of 6.0, 9.0 and 12.0 m/h. There was no significant difference between ripening times for the applied filtration rates. High mass capacity and relatively low head loss growth enabled long filtration runs. To confirm the importance of biological processes in the ripening bed for manganese removal, the third stage of the research was conducted. After the chalcedonite was ripened the bed was disinfected. The manganese concentration in the effluent immediately increased to 0.22–0.28 mgMn/L. To establish the adsorption potential of filtration materials for manganese the Freundlich isotherms were developed for chalcedonite and silica sand. The internal structure parameters (pore surface and volume) of chalcedonite and silica sand were determined using the BET (Brunauer–Emmett–Teller) isotherm method.