Vascular tissues are main routes of resource transport, which are crucial for the growth of fleshy fruit. Very few quantitative data of the total and active areas of xylem and phloem are available for herbaceous plants and their variabilities are unknown. In this study, histological approach and process-based modeling of tomato fruit growth were combined to evaluate the potential contribution of the pedicel anatomy to fruit mass variations. Eleven genotypes were described and the impact of water deficit was studied depending on stress intensity and stage of application. In parallel, MRI experiments allowed to better understand the source of variability in xylem flow along the main stem. Our results suggested that the genetic and water deficit-induced variations in the areas of vascular tissues in the pedicel partly contributed to fruit mass variability. Flow-MRI appeared to be a complementary non-destructive method to phenotype vascular tissues. Whereas the flow velocity in active xylem vessels was rather stable along the main stem, the decrease in the number of active vessels strongly reduces the effective flow from the bottom to the top of the plant. Fruitful interactions between modeling, histology and flow-MRI are promising and worth exploring, to predict water fluxes within plant architecture.