As a result of diverse changes in land use and in water-resource management in the high basin of the Zadorra River (Basque Country), an important loss of water resources and an intense contamination by nitrogen compounds has taken place. The purpose of this paper is to detail the land transformations that have taken place on the aquifer since the 1950s: increase of drainage network, change from dry to irrigated farming, and diversion of rivers at the aquifer unit inlet. Furthermore, we analyze the impact of these transformations on the hydrodynamics and water quality of this aquifer system.