Aeration followed by rapid sand filtration is a common method in drinking water treatment to remove iron (Fe) and manganese (Mn) from anoxic groundwater. To ensure the successful removal of Fe and Mn within a single filter, several factors such as raw water characteristics, backwash procedures and chemical and microbial interactions with the filter medium need to be considered. Here, we assess the characteristics of a single medium rapid sand filter with highly efficient removal of Fe and Mn. Using synchrotron X-ray spectroscopy, we show that formation of ferrihydrite-type Fe oxides in the top of the filter (0–50 cm) accounts for >95 % of the removal of dissolved Fe2+ in the filter. Birnessite-type Mn- oxides, which are thought to be biogenic, form over a wider depth interval (0–110 cm). Results of 16S rRNA gene amplicon sequencing indicate a corresponding distinct vertical stratification of the microbial community, with potential iron-oxidizing Gallionella, Leptothrix and Sideroxydans dominating in the upper part of the filter, and nitrifiers being more prevalent deeper in the filter. Besides Fe and Mn-oxide, Fe-flocs and bacteriological hollow sheets form in the upper part of the filter. Both the Fe-flocs, hollow Fe-sheets and part of the Fe and Mn coatings are removed through backwashing, thereby reducing the pressure difference measured over the filter medium linked to clogging of pores (from 14 kPa to 1.5 kPa) and ensuring continued water flow. Backwashing removes part of the Gallionella, but this does not negatively impact the filter performance. Strikingly, SEM imaging with EDS mapping revealed alternating layers of Fe and Mn-oxides on the coated grains throughout the filter. This indicates slow mixing of the filter medium between the upper 30 cm and the rest of the filter during backwashing. Slow mixing likely contributes to continued success of the filter by ensuring homogeneous filter bed growth, while still allowing for stratification of the microbial community.