Groundwater is an important drinking water source. However, the application of fertilizers in regions with high agricultural activity leads to the contamination of groundwater with nitrate. Nitrate concentrations in groundwater can be reduced by denitrifying microorganisms colonizing different zones of aquifers. Yet, little is known about the microbial key players involved in nitrate turnover in aquifers. In collaboration with a multidisciplinary team of scientist, we study nitrate turnover processes in the anoxic aquifer of the Ammer river and the Bronnbachquelle spring catchments (SW Germany). Using groundwater monitoring wells and by retrieving pristine rock samples through a drilling campaign, we revealed a high abundance of microorganisms that have the potential to couple the oxidation of iron and sulfur to the reduction of nitrate. Collectively, our interdisciplinary findings suggest that nitrate removal in groundwater occurs through a series of microbially driving redox transformations.