Salinity is one of the largest stresses blocking horizontal and vertical expansion in agricultural lands. Establishing salt-tolerant genotypes is a promising method to benefit from poor water quality and salinized lands. An integrated method was developed for accomplishing reliable and effective evaluation of traits stability of salt-tolerant wheat. The study aims were to estimate the genetic relationships between explanatory traits and shoot dry matter (SDM), and determine the traits stability under three salinity levels. Morphophysiological and biochemical traits were evaluated as selection criteria for SDM improvement in wheat for salinity tolerance. Three cultivars and three high-yielding doubled haploid lines (DHLs) were used. Three salt (NaCl) levels (control (washed sand), 7 and 14 dS m−1) were applied for 45 days (at the first signs of death in the sensitive genotypes). All morphophysiological traits gradually decreased as salinity levels increased, excluding the number of roots. Decreases were more visible in sensitive genotypes than in tolerant genotypes. All biochemical traits increased as salinity levels increased. Variance inflation factors (VIFs) and condition number exhibited multicollinearity for membrane stability index and polyphenol oxidase activity. After their removal, all VIFs were <10, thereby increasing path coefficient accuracy. Total chlorophyll content (CHL) and catalase (CAT) provided significant direct effects regarding genetic and phenotypic correlations for the three salinity levels and their interactions in path analysis on SDM, indicating their stability. CHL and CAT had high heritability (>0.60%) and genetic gain (>20%) and highly significant genetic correlation, co-heritability, and selection efficiencies for SDM. CHL and CAT could be used as selection criteria for salinity tolerance in wheat-breeding programs. The tolerated line (DHL21) with the check cultivar (Sakha 93) can be also recommended as novel genetic resource for improving salinity tolerance of wheat.