The purpose of this study is to obtain a better understanding of groundwater contamination processes in an arid environment (precipitation of 50 mm/year) due to cultivation. Additional aims were to study the fate of N, K, and other ions along the whole hydrological system including the soil and vadose zone, and to compare groundwater in its natural state with contaminated groundwater (through the drilling of several wells). A combination of physical, chemical, and isotopic analyses was used to describe the hydrogeological system and the recharge trends of water and salts to the aquifers. The results indicate that intensive irrigation and fertilization substantially affected the quantity and quality of groundwater recharge. Low irrigation efficiency of about 50% contributes approximately 3.5–4 million m3/year to the hydrological system, which corresponds to 0.65 m per year of recharge in the irrigated area, by far the most significant recharge mechanism. Two main contamination processes were identified, both linked to human activity: (1) salinization due to circulation of dissolved salts in the irrigation water itself, mainly chloride, sulfate, sodium and calcium, and (2) direct input of nitrate and potassium mainly from fertilizers. The nitrate concentrations in a local shallow groundwater lens range between 100 and 300 mg/l and in the upper sub-aquifer are over 50 mg/l. A major source of nitrate is fertilizer N in the excess irrigation water. The isotopic compositions of δ15N–NO3 (range of 4.9–14.8‰) imply also possible contributions from nearby sewage ponds and/or manure. Other evidence of contamination of the local groundwater lens includes high concentrations of K (20–120 mg/l) and total organic carbon (about 10 mg/l).