The aim of this study was to assess some physiological parameters and anatomical changes in two wheat plant cultivars (Triticum aestivum L. cvs. Sakha 93 and Sids 9) in response to irrigation with magnetized water under two levels of drought stress (field capacity (FC) of 75% and 50%) and the control (FC 100%) in two consecutive winter growing seasons (November 20 to May 5 2014/2015 and 2015/2016). Pot experiments were carried out in a greenhouse in the experimental farm of the Faculty of Agriculture, Menoufia University, Shibin El-Kom, Egypt. A water deficit, particularly at 50% FC, significantly decreased growth and parameter values, above all in Sakha 93, and disrupted most physiological aspects, biochemical constituents and internal structural features of both wheat cultivars. Irrigation with magnetized water alleviated the negative consequences of drought stress on most physiological and biochemical parameters to a variable extent: the whole plant dry weight, total water content, total soluble sugar concentration in leaves, total free amino acids and proline increased by about 32, 12, 17, 27 and 73%, respectively, under 50% FC drought stress in Sids 9 compared to the control. As the levels of drought increased, the grain yield (g/plant) decreased considerably, from about 81% in Sakha 93 at 50% FC to 26% in Sids 9 at 75% FC. The use of magnetic water increased grain yield from 61% in Sakha 93 at 75% FC to about 268% in Sids 9 at 50% FC. Magnetic water also increased the thickness of the flag leaf midvein and lamina, as well as the metaxylem vessel diameter of Sakha 93 by 28.8, 11.7 and 20.0%, respectively, compared to the control. The application of magnetic water increased the growth and the other parameter values studied in both cultivars but above all in Sakha 93, whereas Sids 9 produced more grain yield under all levels of drought stress. As the growth and grain production increased in both cultivars when using magnetic water, this study recommends this type of irrigation for these wheat plants, which are widespread in Egypt