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Pecan [Carya illinoensis (Wanngenh) K. Koch] is one of the most important nut crops in arid and semiarid regions of Mexico. Here, most pecans are grown in saline soils having poor permeability which are further degraded by the use of low-quality irrigation water. Salinity adversely affects both pecan nut quality and yield. Little work has been done to explore the physiological effects of salinity on native pecan trees. Here we examine physiological changes determined by exposure of pecan seedlings to sodium sulfate (Na2SO4) at four concentrations: 1000, 2000, 3000 and 4000 mg/L applied twice weekly over a 70 d period. Control plants were similarly irrigated but with water free of Na2SO4. The aim was to identify and quantify the putative salinity damage to native pecan seedlings growing in Chihuahua, Mexico. Seedlings exposed to Na2SO4 were of reduced height and stem diameter. At the highest exposure level (4000 mg/L), proline concentration in the leaflets was 820% higher (2.63 mg/g) than in the controls (0.32 mg/g), and chlorophyll was 35% lower (23.4 mg/L) than in the controls (36 mg/L). Meanwhile, sulfate ion concentration was increased by 104% from 84.47 to 172.5 mg/g. Root biomass decreased by 310% (from 30.5 to 9.5 g) and foliar biomass decreased by 260% (from 26.7 to 10 g). No disease symptoms were apparent in any seedlings suggesting that these changes were induced by Na2SO4 stress alone. Of the physiological parameters measured, proline, chlorophyll and sulfate ion concentration, as well as root and shoot biomasses were strongly affected by irrigation with Na2SO4 at concentrations of 2000 mg/L and above.