Nitrogen (N) source is known to affect ion composition and organic acid production in plants. We determined the effects of N source and nitrification inhibitors (NI) on soil solution ionic composition and nutrient availability, grapefruit yield and quality, and accumulation of carboxylic acids in fruits as expressed by fruit acidity. The individual and combined effects of N source (fertilizers or effluent) and NI on mature grapefruit trees were studied in a commercial orchard planted on a sandy loam soil and drip-fertigated. Fertilization with ammonium sulfate (AS) resulted in soil acidification during the irrigation season from pH 7.4 to 6.1, and increased P, Mn and Ca concentrations in the soil solution relative to the ammonium nitrate (AN) treatment. Consequently, under AS treatment, P and Mn uptake, chlorophyll content in leaves and fruits, total soluble solids (TSS) in fruits, were higher than in the other treatments. Excess ammonium concentration in the soil solution inhibited Ca and K uptake without significantly reducing fruit acidity. The positive correlation found between Ca in leaf and yield was unexpected since the soils are calcareous. The presence of dissolved organic N in the effluent treatment diminished the impact of ammonium on soil pH. Application of NI had a negligible effect on fruit yield and quality but enhanced the capacity of AS to raise N uptake above that achieved with AN or effluent. Consequently, it reduced the potential for N leaching from the soil.