The average nitrate concentration in the groundwater of the Vitoria-Gasteiz (Basque Country) quaternary aquifer rose from 50 mg NO3-/l during 1986 to over 200 mg/l in 1995, which represents an increase of some 20 mg NO3-/l per year. From 1995 to 2002, the nitrate concentration of the groundwater slightly decreased. Nitrate groundwater pollution during the period 1986-1993 was the result of the abusive use of fertilizers and of the modification in the recharge patterns of the aquifer from surface water sources. From 1993 onwards, apart from a possible rationalization in fertilizer use, the change in the origin of water for irrigation and wetland restoration (water is taken now from artificial pools outside the quaternary aquifer) must be explained in order to account for the observed decrease in nitrate concentration in the groundwater. The water of the aquifer and of the unsaturated zone were studied in two experimental plots (one of them cultivated and the other uncultivated) for 18 months (January 1993-June 1994), during the period of maximum contamination, to evaluate the effect of fertilizers on soil water and on the water in the saturated zone. The soil water was sampled using soil lysimeters at various depths. The volumetric water content of the soil was measured at the same depths using time domain reflectrometry (TDR) probes. Samples of groundwater were taken from a network of wells on the aquifer scale, two located close to the two experimental plots. The temporal evolution of nitrate concentrations in soil solutions depends on the addition of fertilizers and on soil nitrate leaching by rain. During episodes of intense rain (>50 mm in a day), the groundwater deposits are recharged with water coming from the leaching of interstitial soil solutions, causing an increase in the groundwater nitrate concentrations. The mass of nitrate leached from the cultivated zone is five times higher than that of the nitrate leached from the uncultivated zone (1147 kg NO3-/ha in the cultivated sector as against 211 kg NO3-/ha in the uncultivated sector), although part of the nitrate leached into the soil had been previously deposited by the rise of the water table. If we consider that the level of groundwater input is similar in both plots, we may conclude that 964 kg NO3-/ha circulated towards the groundwater in the cultivated zone during the period under study, representing 87% of the nitrate applied to the soil in the form of fertilizer during that period.