Use of saline water in agriculture is necessary because of limited fresh water resources. The study was carried out to evaluate the effect of water quality and organic and chemical fertilizers on content nutrients, ash in seed and chlorophyll index of borage. The experimental design was a split plot with two irrigation sources: irrigation with fresh and saline well-water comprising the main-plots, and four fertilization systems: application of NPK at 80:40:30 kg ha^-1, 40000 kg ha^-1 of manure, NPK at 40:20:15 kg ha^-1 plus 20000 kg ha^-1 of manure and no soil fertility as sub-plots that were applied with three replications. The experiment was conducted in 2012 growing season at the Research Farm in Zabol University, Iran. Salt irrigation water significantly increased concentration of ash, chlorine and sodium in seeds. The low quality of irrigation water reduced nitrogen, phosphorus, magnesium, potassium and calcium in seeds. Application of fertilization significantly increased all studied traits compared with the control except magnesium. Combinations of organic and inorganic fertilizer were more effective from sole application. Interaction of water quality with different systems of fertilization was significant on the concentrations of sodium, chloride, calcium and chlorophyll index; therefore the combination of organic and chemical fertilizer not only reduced. The concentration of elements that create salt damage (sodium and chloride), but also improved the absorption of macronutrients.