Wheat (Triticum aestivum) is one of the most important cereal crops in the world. However, drought is a serious factor facing wheat farmers worldwide and causing substantial yield loss. Therefore, the aim of this study is to determine if particular compounds were produced during times of water stress thereby enabling the plant to cope. The vacuolar compounds in the stems, leaves, and flower spikes of water-stressed and unstressed McNeal and Thatcher varieties were analyzed using HPLC and compared for differences and/or similarities. The stems, leaves, and flower spikes of both varieties showed mainly phenolic compounds including phenyl propenoids and flavonoids. Of the phenyl propenoids, chlorogenic acid was prevalent, and, of the flavonoids, luteolin glycosides were dominant. Apigenin was also present in the flavonoids. However, further analyses indicate that the concentrations of luteolin and apigenin were frequently higher in the water stressed varieties compared to the unstressed varieties. In contrast, chlorogenic acid concentrations were frequently higher in the unstressed varieties. This fluctuation in concentration of luteolin, apigenin, and chlorogenic acid could be a coping mechanism used by the plant to deal with water stress.