This study was carried out during the two consecutive seasons of 2012 and 2013 in shade house for Plant Production Dept. Fac. Environ. Agri. Sci. Suez Canal Univ. Egypt. Two citrus six-month-old uniform seedling citrus rootstocks namely: Sour orange and Volkamer lemon transferred into black plastic tube PVC (15 cm diameter x 40 cm depth) filled with 2kg growth media mixture of sand soil and peat moss (4:1 by volume) and irrigated using the tap water at 14 days before run treatments. These seedlings were subjected to three different irrigation saline water levels (tap water 700 "control", 2000, and 3000 ppm) to determine the effects of water salt level on growth parameters, chemical compositions, leaf total pigments and proline. The results obtained showed that Volkamer lemon seedlings had the greatest leaf and root biomass, photosynthetic pigments, proline, leaf k content and area of root vascular bundle and had the lowest values leaf N, Cl and Na content, thickness of root cortex, thickness of mesophyll tissue and leaf blade, while Sour orange seedlings were on the contrary. On the other hand, irrigation with the saline water caused decrease the all vegetative growth parameters, plant photosynthetic pigments and area of root vascular cylinder, while increased the leaf N, Cl and Na content, leaf proline concentration and thickness of root cortex, thickness of mesophyll tissue and leaf blade. Finally, vegetative growth parameters, leaf mineral and leaf total pigments analysis and anatomy features for root and leaf blade indicated that Volkamer lemon rootstock is more tolerant to salinity of irrigation water.