Salinity responses and salinity-related suppression of budbreak of drip-irrigated pecan [Carya illinoinensis (Wangenh.) K. Koch] seedlings under different irrigation water salinity (ECIRR) levels were investigated in the pot-in-pot system. The 1-year-old pecan seedlings of rootstock ‘Riverside’ grafted with ‘Western Schley’ scions were transplanted in pots filled with sandy loam soil and grown for 2 years under the same amount of irrigation water but four irrigation ECIRR treatment levels consisting of 1.4 dS·m−1 (control), and three qualities of irrigation water obtained by using a solution of calcium chloride (CaCl2) and sodium chloride (NaCl) in a ratio of 2:1 (by weight) to reach the ECIRR levels of 3.5, 5.5, and 7.5 dS·m−1, respectively. The leachate electrical conductivity (ECd) was highly correlated with soil salinity (EC1:1) and was significantly higher when the irrigation ECIRR treatment levels increased from 1.4 (control) to 7.5 dS·m−1. However, both ECd and EC1:1 remained nearly constant within the same irrigation ECIRR treatment level during both years. Increasing salinity in irrigation water, particularly the ECIRR levels of 5.5 and 7.5 dS·m−1, showed significantly low seedling height and stem diameter growth and delayed or even inhibited budbreak in the seedlings. The EC1:1 that inhibited seedling heights, stem diameters, and budbreak was somewhere between 0.89 and 2.71 dS·m−1 (or ECIRR between 1.4 and 3.5 dS·m−1 and ECd between 2.10 and 4.86 dS·m−1), providing that soil water content was not a limiting factor in the root zone and irrigation water was uniformly distributed in the confined root zone to obtain uniform salt leaching. The visual symptoms of leaf scorch for irrigation ECIRR levels of 3.5, 5.5, and 7.5 dS·m−1 also indicated that somewhere between 0.89 and 2.71 dS·m−1 of the EC1:1, salt injury started to occur. Increasing salinity in irrigation water significantly increased chloride (Cl–) accumulation but reduced nitrogen (N) content in the scorched leaves, particularly under the irrigation ECIRR levels of 5.5 and 7.5 dS·m−1. Leaf scorch symptoms in pecan seedlings were likely associated with Cl– toxicity. No pecan seedlings under the irrigation ECIRR treatment levels of 5.5 and 7.5 dS·m−1 survived to the end of the 2-year growing period. Thus, threshold EC1:1 was somewhere between 0.89 and 2.71 dS·m−1 beyond which plant injury increases with increasing EC1:1 threatening the survival of pecan seedlings.