Water scarcity and soil carbon dioxide elevation in arid regions are considered the most serious factors affecting crop growth and productivity. This study aimed to investigate the impacts of elevated CO2 levels (eCO2 at rates of 700 and 1000 ppm) on agro-physiological attributes to induce drought tolerance in cucumbers by activating the expression of genes related to aquaporin and stress response, which improved the yield of cucumber under two levels of irrigation water conditions [75% and 100% crop evapotranspiration (ETc)]. Therefore, two field experiments were conducted in a greenhouse with controlled internal climate conditions, at the Mohamed Naguib sector of the national company for protected agriculture, during the winter seasons of 2021–2022 and 2022–2023. The treatments included eCO2 in soil under normal and partial root zoon drying (PRD, 100% ETc Full irrigations, and 75% ETc). All the applied treatments were organized as a randomized complete block design (RCBD) and each treatment was replicated six times. Untreated plants were designed as control treatment (CO2 concentration was 400 ppm). The results of this study showed that elevating CO2 at 700 and 1000 ppm in soil significantly increased plant growth parameters, photosynthesis measurements, and phytohormones [indole acetic acid (IAA) and gibberellic acid (GA3)], under partial root-zone drying (75% ETc) and full irrigation conditions (100% ETc). Under PRD condition, eCO2 at 700 ppm significantly improved plant height (13.68%), number of shoots (19.88%), Leaf greenness index (SPAD value, 16.60%), root length (24.88%), fresh weight (64.77%) and dry weight (61.25%) of cucumber plant, when compared to untreated plants. The pervious treatment also increased photosynthesis rate, stomatal conductance, and intercellular CO2 concentration by 50.65%, 15.30% and 12.18%; respectively, compared to the control treatment. Similar findings were observed in nutrient concentration, carbohydrate content, Proline, total antioxidants in the leaf, and nutrients. In contrast, eCO2 at 700 ppm in the soil reduced the values of transpiration rate (6.33%) and Abscisic acid (ABA, 34.03%) content in cucumber leaves compared to untreated plants under both water levels. Furthermore, the results revealed that the gene transcript levels of the aquaporin-related genes (CsPIP1-2 and CsTIP4) significantly increased compared with a well-watered condition. The transcript levels of CsPIP improved the contribution rate of cell water transportation (intermediated by aquaporin’s genes) and root or leaf hydraulic conductivity. The quantitative real-time PCR expression results revealed the upregulation of CsAGO1 stress-response genes in plants exposed to 700 ppm CO2. In conclusion, elevating CO2 at 700 ppm in the soil might be a promising technique to enhance the growth and productivity of cucumber plants in addition to alleviating the adverse effects of drought stresses.