Deficit irrigation practices and utilization of rootstocks that are tolerant to water stress are critical strategies for the protection of water resources and sustainable irrigation management, especially in arid and semi-arid areas. Therefore, this study was carried out to investigate the yield and quality of watermelon grafted onto different rootstocks under deficit irrigation conditions during 2017 and 2018 in the Konya Plain of Turkey, where the semi-arid climate is prevalent. In this study, five different plant materials, such as citroides1 (A1), citroides2 (A2), gourd (A3), hybrid TZ148 (A4) rootstocks grafted with the Crimson Tide variety, and non-grafted Crimson Tide as control (K1), were used as the main-plots. Five different irrigation levels, calculated by taking into account the amounts of cumulative water (Ep) that evaporated at 7-day intervals from Class A Pan (I100 = 1.00Ep; I75 = 0.75Ep; I50 = 0.50Ep; I35 = 0.35Ep, and I0 = rain-fed), were used as the sub-plots. When the average of experimental years was considered, the highest rate of evapotranspiration (ET) was found in the plot A4I100 (615 mm). The highest fruit yield was obtained from the A4I100 (93.4 t/ha), and an increase in yield of up to 35 % was achieved in the A4I100, compared to non-grafted plants applied I100 irrigation level (K1I100). The analysis of data by both separate evaluation and principal component analysis (PCA) revealed that the yield values obtained from plants grafted onto A4, A1, and A2 rootstocks applied I75 irrigation level were higher than non-grafted plants applied I100 irrigation level. The water productivity (WP) and irrigation water productivity (IWP) ranged between 7.1–17.4 kg/m3 and 11.7–25.0 kg/m3, respectively, and a significant increase in the values of WP and IWP was achieved by grafting. This two-year study revealed that the performances of citron watermelon rootstocks were found close to the TZ148 rootstock in terms of fruit yield, certain yield components, WP, and IWP. Thus, it has also been demonstrated that the citron watermelons could be used commercially as watermelon rootstocks, and citron watermelon rootstocks could be used as watermelon rootstocks in breeding programs, in order to save water, especially in arid and semi-arid regions.