Currently, many techniques to alleviate the negative effects of water stress, specifically drought, on plants are frequently the subject of research. In this study, the effects of two different plant growth-promoting rhizobacterial (PGPR) species isolated from arid and semiarid areas whose activities under water stress were determined in a preliminary study on several physiological properties and nutrient uptake of watermelons grafted onto different rootstocks were investigated under deficit irrigation. In this study, the performance of two PGPRs (B1: Paenarthrobacter aurescens and B2: Pseudarthrobacter polychromogenes) inoculated into ungrafted watermelon (R0 (Citrullus lanatus (Thumb.) Matsum and Nakai cv. Crimson Tide, CT)) and grafted watermelons (R1: CT grafted onto citron watermelon rootstock (Citrullus lanatus var. Citroides) and R2: CT grafted onto the hybrid rootstock TZ-148 (Cucurbita maxima Duchesne × Cucurbita moschata Duchesne)) were studied under different irrigation levels. Severe water stress negatively affected the physiological characteristics, such as stomatal conductance (gs) and photosynthesis efficiency (QPSII), of watermelon plants. Moreover, the contents of leaf mineral nutrients such as N, P, and K decreased significantly with increasing water stress. On the other hand, rootstocks improved the performance of sweet watermelon in terms of macronutrients such as N, K, and Mg and micronutrients such as Fe and Cu. Moreover, the drought-tolerant rootstocks (R1 and R2) used in this study protected watermelon plants against the negative effects of water stress by reducing gs compared to that of ungrafted plants. Moreover, although rhizobacteria did not have a significant effect on the gs, QPSII, or leaf water potential (LWP) of watermelon, they enhanced the uptake of minerals such as macro- and micronutrients from the soil by plants. Under full irrigation and particularly deficit irrigation, P. polychromogenes (B2) increased the contents of macronutrients such as Mg and K, while P. aurescens (B1) increased the contents of micronutrients such as Fe, Cu, Mn, and B in watermelons. Our results revealed that these two rhizobacterial species, which were isolated from arid and semiarid areas, contribute to the nutrient uptake of watermelon plants grown under water stress.