Drought stress is a major factor limiting wheat crop production worldwide. The application of humic acid (HA) and the selection of the appropriate genotype in the suitable site is one of the most important methods of tolerance of wheat plants to drought-stress conditions. The aim of this study was achieved using a three-way ANOVA, the stress tolerance index (STI), the Pearson correlation coefficient (rp), and principal component analysis (PCA). Three field experiments in three sites (Al-Qasr, El-Neguilla, and Abo Kwela) during the 2019/21 and 2020/21 seasons were conducted, entailing one Egyptian bread wheat variety (Sakha 94) with three HA rates (0, 30, and 60 kg ha−1) under normal and drought-stress conditions (supplemental irrigation). According to the ANOVA, the sites, supplemental irrigation, HA rates, and their first- and second-order interactions the grain yield and most traits evaluated (p ≤ 0.05 or 0.01) were significantly influenced in both seasons. Drought stress drastically reduced all traits registered in all factors studied compared with normal conditions. The wheat plants at the Al-Qasr site in both seasons showed significantly increased grain yield and most traits compared with that of the other sites under normal and drought-stress conditions. HA significantly promoted all studied traits under drought stress, and was highest when applying 60 kg HA ha−1, regardless of the site. The greatest grain yield and most traits monitored were observed in wheat plants fertilized with 60 kg HA ha−1 at the Al-Qasr site in both seasons under both conditions. Grain yield significantly (p ≤ 0.05 or 0.01) correlated with water and precipitation use efficiency as well as the most studied traits under normal and drought-stress conditions. The results of STI, rp, and PCA from the current study could be useful and could be used as a suitable method for studying drought-tolerance mechanisms to improve wheat productivity. Based on the results of statistical methods used in this study, we recommend the application of 60 kg HA ha−1 to improve wheat productivity under drought conditions along the north-western coast of Egypt.