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Water and salinity are main co-occurring stresses affecting plant growth and development in arid lands. In this study interactive effects of water and salinity stresses on Balanites aegyptiaca seedlings from three different sources (SD5.1, SD6.2 and KSA) were assessed in potted experiment under greenhouse conditions. The effect was measured on stomatal conductance (G(s)), specific leaf area (SLA), seedling quality (Shoot to Root ratio (SIR), Dickson Quality Index (DQI) and Sturdiness Quotient (SQ)), Nutrient uptake (N content, K/Na and Ca/Na ratios) and growth. The seedlings were either watered twice a week (well watered) or every two weeks (water stressed), in addition to four salt concentrations (fresh water as control, 5 dS m(-1), 7 dS m(-1) and 9 dS m(-1) EC). Water and salinity stresses resulted in reduced G(s), SLA, DQ, SQ and SIR, associated with lower height and root collar diameter. However, irrespective of salt concentration, water stressed seedlings displayed substantial reduction in G(s), indicating that G(s) is among the most important water conservation strategy for this species. SIR also, remarkably decreased in water stressed seedlings, but, within watering treatment it was increased with increasing salt concentration. SLA and DQI were more affected by salinity stress, due to the increased leaf weight with increasing salinity. N content was more sensitive to water stress than salinity. Both Ca/Na and K/Na ratios were decreased with increasing salt concentration. The three sources exhibited significant variation in their response to water and salinity stresses. SD5.1 displayed higher values in most of studied traits. G(s) and S/R may be considered as fitness responses of this species to water stress, while DQI, SLA and K/Na can serve as good indicators to measure response to salt stress.