This study reports the impact of hydrological conditions on salinisation and nitrate concentrations of a coastal aquifer located at the Mediterranean Sea, southern Spain. Eighty-two samples of ground- and surface water taken during two extreme hydrological events between 1994 and 1996 at 25 different wells were evaluated with regard to hydrochemistry, focusing on nitrate concentrations and salinisation, which constitute the main hazard of this aquifer. Furthermore, hydrochemical data were analysed by principal component analysis (PCA). Additionally, in 2007 13 ground- and surface water samples taken at 12 different locations were analysed for stable isotopes of D/18O, and one sample was analysed for 15N. Since 1993 until present saltwater intrusion was observed only during dry hydrological conditions in 1994; it showed an irregular salinisation pattern probably related to locally elevated hydraulic conductivities. Nitrate concentrations increase significantly during wet hydrologic conditions owing to uptake of nitrate by rising groundwater. Stable isotopes of groundwater reveal an Atlantic origin of the precipitation that recharges the aquifer and a minor amount of groundwater recharge by the water coming from the La Viñuela reservoir, which is used for irrigation over the aquifer. 15N isotopes point to a considerable input of nitrates derived from organic fertilisers. © Springer-Verlag 2009.