Owing to geological structural factors, the groundwater in some areas naturally contains iron and manganese concentrations much higher than the permissible limits. In this study, scoria, a natural silicate mineral, was used to remove iron and manganese from water. For this purpose, filtration and cultivation of microorganisms were performed. The properties of scoria were characterized using BET, XPS, and SEM analyses, and the results showed that scoria is effective for iron and manganese removal. The mesoporous structure of scoria provides basic conditions for iron and manganese removal, and the high surface area provides a large number of adsorbent active sites. The surface of scoria showed significant changes after the experiment. Mn²⁺ adsorbed on the scoria surface was in the oxidized form, and adsorbed Fe²⁺ mainly existed as precipitates and colloids. Isolating and cultivating functional bacterial experiments indicated that some microorganisms exist in groundwater that contribute to the removal of iron and manganese; these iron and manganese bacteria, such as gallionella, exiguobacterium and citrobacter, could effectively remove iron and manganese under different initial concentrations of both. Overall, scoria was found to be a promising material for the removal of excessive iron and manganese from groundwater, thus serving as a meaningful reference for drinking water treatment by natural materials.