In the present article, the treatment of groundwater containing Mn(II) and Fe(II) has been investigated. The biological oxidation of Mn(II) and Fe(II) in upflow filtration units comprised the applied experimental technique. The oxidation processes were mediated by specific bacteria, namely the Leptothrix ochracea and Gallionella ferruginea, which belong to the general category of manganese and iron oxidizing bacteria. This work was focused on the characterization of the products of biological oxidation and to the examination of the kinetics of Mn(II) removal as compared with Fe(II) removal from groundwaters. The products of biological oxidation were characterized using the spectroscopic techniques XRD, XPS and SEM-EDS and comprised a mixture of biogenic hydrous manganese and iron oxides. The oxidation state of manganese in the precipitates was found to be between 3 and 4. Iron oxides were mainly in the form of amorphous ferrihydrite. The kinetic results indicated that the rates of manganese and iron oxidation were several orders of magnitude greater than the respective for abiotic oxidation. The bacterially mediated oxidation of iron was faster than manganese oxidation, presenting half-lives of reaction 0.9 and 3.98 min, respectively.