The aim of the present study was to determine whether grafting could improve alkalinity tolerance of watermelon, and to study the changes induced by the rootstock in the shoot growth at agronomical, physiological, and biochemical levels. Two greenhouse experiments were carried out to determine growth, net photosynthetic rate, electrolyte leakage, root Fe(III)-chelate reductase (FCR) activity, mineral composition and assimilate partitioning (experiment 1, 2007), and organic acid concentration in root exudates (experiment 2, 2008), of watermelon plants [Citrullus lanatus (Thumb.) Matsum. and Nakai cv. ‘Ingrid’] either ungrafted or grafted onto the four commercial rootstocks: ‘Macis’, ‘Argentario’[Lagenaria siceraria (Mol.) Standl.] and ‘P360’, ‘PS1313’ (Cucurbita maxima Duchesne × Cucurbita moschata Duchesne) grown in a closed-loop system. Plants were supplied with nutrient solutions having two levels of pH (6.0 or 8.1). The high pH nutrient solution had the same basic composition plus an additional of 10 mM NaHCO3 and 0.5 g L−1 CaCO3. Significant depression of shoot, root biomass production, and leaf macro- (N, P, K, and Mg) and microelements (Fe, Mn, Zn, and Cu) under high pH level was observed in both grafted and ungrafted plants. Increasing the concentration of NaHCO3 from 0 to 10 mM in the nutrient solution significantly enhanced FCR activity of root tips to 2.3 times in high pH treatment in comparison to the control. At high pH level, the percentage of shoot biomass weight reduction was significantly lower in plants grafted onto pumpkins rootstocks in comparison to those grafted onto the bottle gourd rootstocks and the ungrafted plants. Moreover, at high pH level, the highest percentage of root biomass weight reduction was recorded in both grafting combinations ‘Ingrid/P360’ and ‘Ingrid/Macis’. The high pH-related reduction in net assimilation was more severe in ungrafted plants in comparison with the grafted ones. The Fe concentration in leaves was significantly higher in plants grafted onto pumpkin rootstocks (avg. 109.5 μg g−1) in comparison to that of bottle gourd rootstocks and ungrafted plants (avg. 86.7 μg g−1). For plants grafted onto bottle gourd rootstocks and ungrafted plants the high pH level (8.1) in the nutrient solution caused significant decrease in macronutrient leaf concentration especially for P and Mg compared to plants grafted onto pumpkin rootstocks. Increasing the nutrient solution pH from 6.0 to 8.1 increased exudation of organic acids (citric, malic, tartaric and succinic acids). Watermelon plants grafted onto pumpkin rootstocks exuded more citric and malic acids than those grafted onto bottle gourd rootstocks and ungrafted plants especially under bicarbonate-enriched conditions. These results support the hypothesis that uptake of nutrients (e.g. P, Mg, and Fe) from the nutrient solution by pumpkin rootstocks was facilitated by exudation of organic acids from roots.