Common bean productivity in arid and semi-arid regions is frequently constrained by water deficit and micronutrient limitations. This study aimed to (i) quantify the effects of deficit irrigation and foliar micronutrient application on growth, yield, and water productivity, and (ii) elucidate the physiological and biochemical mechanisms underlying genotype-specific drought tolerance. Field experiments were conducted over two growing seasons on sandy soil using three common bean varieties (Nebraska, Giza 3, and Giza 6). Treatments were arranged in a split-split-plot randomized complete block design, with varieties as main plots, irrigation regimes [full irrigation (F100%), moderate deficit (D80%), and severe deficit (D70%)] as subplots, and foliar-applied micronutrients (Fe, Zn, and Mn at three rates) as sub-subplots. Measurements at mid- and late-growth stages included chlorophyll content, antioxidant enzyme activity, leaf micronutrient concentrations, growth traits, grain quality, yield, and water productivity. Giza 6 exhibited superior early physiological responses, with significantly higher chlorophyll content and antioxidant enzyme activity under the highest micronutrient rate (T3: 15 Fe : 30 Zn : 20 Mn). Under prolonged deficit irrigation, the combination of moderate stress (D80%) and T2-T3 applications sustained higher leaf Fe, Zn, and Mn concentrations, supporting continued growth and nutrient translocation. Clear genotypic differences were observed, with Giza 6 maintaining higher grain quality, yield, and water productivity under water-limited conditions, whereas Nebraska showed greater sensitivity despite micronutrient supplementation. These findings demonstrate that integrated water-nutrient management enhances drought resilience through improved physiological stability and nutrient homeostasis. Combining moderate deficit irrigation with targeted micronutrient application is an effective strategy to optimize productivity and water use efficiency in drought-prone environments.