Long-term application of fertilizer and manure may change soil fertility, crop yield, N uptake efficiency, and nitrate and chloride leaching to underground water. The objectives were to quantify those aspects in a long-term (35-year) permanent plots field experiment in a typical arid zone (~250 mm rain) soil, and suggest fertilization and manuring regimes leading to reduced aquifer pollution by nitrate and chloride without compromising crop yield and soil sustainability. Results proved that mineral-N application exceeding plant demand leached, subject to recommended irrigation plus rainfall, below 4 m, thus becoming a potential underground water pollution hazard. Leaching was significantly reduced by partially replacing fertilizer-N by manure-N, with negligible adverse effect on crop yield. Under ample manure (M2) and mineral N (N3) supply (treatment M2N3), the estimated cumulative (35-year) NO3– leaching was 557 g N/m2 and the corresponding Cl– leaching 4097 g Cl–/m2. In treatment M2N0 the corresponding leaching was 0 and 4135 g/m2. The cumulative solute leaching depth was estimated to be 66 m in treatment M2N3 (that gave maximum fruit and dry matter yield) and 125 m in treatment M0N0 (minimum fruit and dry matter yield). Soil cultivation and cropping for 35 years had negligible effect on the plants’ response to fertilizer level and on the soil mineralogical composition.