Drought and salinity are significant stressors for crop plants, including wheat. The relationship between physiological mechanisms and gene expression is important for stress tolerance. NAC transcription factors (TFs) play vital roles in abiotic stress. In this study, we assessed the expression of four TaNAC genes with some physiological traits of nine Egyptian wheat genotypes under different concentrations of PEG and NaCl. All the physiological traits that we assessed declined under both stress conditions in all genotypes. In addition, all the genes that we measured were induced under both stress conditions in young leaves. Shandaweel 1, Bani Seuf 7, Sakha 95, and Misr 2 genotypes showed higher gene expression and were linked with a better genotypic performance in physiological traits under both stress conditions. In addition, we found an association between the expression of NAC genes and physiological traits. Overall, NAC genes may act as beneficial markers for selecting for genotypic tolerance to these stress conditions in wheat.