Detailed full-scale groundwater monitoring was carried out over a period of nine years, sampling at selected points along the groundwater flow direction in its final stretch. This established the hydrogeochemical evolution along the flow of a natural system formed by a calcareous aquifer which discharges and then passes through a quaternary aquifer of lake origin which is rich in organic matter. This evolution is highly conditioned by the oxidation of pyrites that are abundant in both aquifers. In the first aquifer, one kilometre before the discharge location, oxidizing groundwater crosses a pyrite mineralization zone whose oxidation produces an important increase in sulphates and water denitrification over a short period of time. In the quaternary aquifer with peat sediments and pyrites, water experiences, over a small 500 m passage and residence time of between three and nine years, a complete reduction by way of pyrite oxidation, and a consequent increase in sulphates and the generation of hydrogen sulphuric acid. This is an example of an exceptional natural hydrogeological environment which provides guidance on hydrogeochemical processes such as denitrification.