Drought has emerged as a significant abiotic stress in vegetable production. Sweet watermelon (Citrullus lanatus var. lanatus) is susceptible to drought stress (DS) and requires adequate irrigation for optimal yield and quality. The current study sought to shed light on the potential of citron watermelon as a rootstock for watermelon by studying changes in its morphological and physio-biochemical features under deficit irrigation. Crimson Tide F1 (CT) was grafted onto ten morphologically distinct citron watermelon (CW) rootstocks, with Strong Tosa (ST) commercial rootstocks and nongrafted (NG) and self-grafted (SG) Crimson Tide F1 serving as plant material. We used three irrigation (I) levels (I100, I75, and I50) while investigating multiple agronomic and biochemical properties. Increasing water stress negatively affected several plant growth parameters in watermelon. Furthermore, I50 inhibited photosynthesis and pigment content, increasing malondialdehyde (MDA), hydrogen peroxide (H2O2), leaf temperature, and membrane permeability. I50 significantly reduced stomatal conductance and leaf relative water content. Rootstocks responded differently to irrigation regimes and had varying water use efficiency (WUE). Based on the evaluated parameters, we classified ST, CW9, CW16, and CW17 as tolerant; CW4, CW6, CW8, CW11, CW13, CW14, and CW15 as moderately tolerant; and CT as highly susceptible. Combining I75 and citron rootstock will benefit targeted watermelon production and provide significant water savings for sustainable agriculture.