Drought is widely recognized as one of the most significant agricultural constraints worldwide. A strategy to avoid the adverse effects of drought on crops is to cultivate high-yielding varieties by grafting them onto drought-tolerant rootstocks with a differentiated root system. Thus, the objective of this study was to evaluate fruit yield and quality, root system architecture, and water productivity of watermelon grafted onto Lagenaria siceraria rootstocks. To do so, a commercial watermelon cultivar “Santa Amelia” [Citrullus lanatus (Thunb.)] was grafted onto five L. siceraria rootstocks: ‘Illapel’, ‘Osorno’, ‘BG-48’, ‘GC’, and ‘Philippines’, which were grown under three irrigation treatments (100%, 75%, and 50% of evapotranspiration). The comparison of the L. siceraria rootstocks in the irrigation treatments demonstrated no significant effect on watermelon fruit quality parameters. The rootstocks ‘Illapel’, ‘Osorno’, and ‘GC’ significantly improved the fruit number and yield (total fruit weight) under water deficit. Similarly, ‘Illapel’, ‘Osorno’, and ‘GC’ consistently showed statistical differences for root system architecture traits compared to ‘BG-48’ and ‘Philippines’. Based on these results, we concluded that the used L. siceraria rootstocks did not affect the fruit yield and quality of grafted watermelon under water deficit. This study may help adjust the amount of applied water for watermelon production where L. siceraria rootstocks are utilized.