Groundwater is an excellent source for the production of drinking water due to its low concentration of microorganisms and contaminants. The main contaminants present in groundwater are iron, ammonium and manganese, which are sequentially removed in rapid sand filters by a combination of biological and chemical processes. Currently, limited knowledge of the removal mechanisms challenges the design of new drinking water treatment plants (DWTPs). As a result, different treatment schemes are used to treat groundwater with a similar composition. We hypothesize that the difference in plant configuration does not affect the stratification of removal processes. In the present work, the spatial distribution of taxonomic and functional microbiological profiles and physical-chemical removal mechanisms were investigated in two DWTPs with similar incoming water but different treatment schemes. One plant employs a dual bed filter, while the other uses two sequential filters. Concentration profiles and composition of the coating on the sand showed sequential removal of iron and manganese, while ammonium removal was ubiquitous. Activity batch tests revealed section-specific manganese removal mechanisms: adsorption in the first section and oxidation in the second section. The latter is the dominant process in full-scale filters. Manganese oxidation capacity remained constant over the height of the second section. Contrarily, ammonia removal was highly stratified in there. The highest ammonium removal rates were observed at the top section of the filter. Furthermore, ammonium removal rates were higher in the second section compared to the first one. In accordance, metagenomic analysis revealed higher abundances of nitrifying organisms in the second sections. Besides, co-existence of nitrifiers and iron-oxidizers was observed in the top layer, in contrast to the common opinion that iron removal has to be complete before nitrification can start. We (i) conclude that similar distributions in removal mechanisms and genomic profiles were observed in both DWTPs, regardless of plant configuration, (ii) provide the first holistic quantitative analysis of the biological and chemical reactions in full-scale rapid sand filters and, (iii) to our knowledge, prove for the very first time that iron hydroxides on the sand grains adsorb manganese under aerobic conditions, using both adsorption and desorption tests.