Responses of plants to environmental stresses throughout growth and development are highly sensitive to their water and carbon status. Fruit growth and composition depend on availability of resources and their distribution within the network of source and sink organs. Because sap flow provides mineral nutrients and water to sink organs, there is a need to quantify it spatially and temporally in order to better understand fruit growth regulation under fluctuating environment. Nuclear Magnetic Resonance Imaging (MRI) is a direct and noninvasive method allowing the study of cell water balance and phloem and xylem transports in large plants. The objective of this study was to understand and quantify sap flow in the tomato plant architecture in response to water deficit, by combining MRI, histological observations and modeling. Histological measurements were done at the pedicel level to quantify the cross-sectional area of the conductive tissues in response to water deficit. Our measurements were compared to the predictions of a biophysical model that simulates fruit growth. Measurements of sap flow were done by implementing a novel flow-MRI method. MRI experiments were conducted at 9.4T, using inflow and outflow sensitive spin echo pulse sequences. These methods were applied to estimate sap fluxes in the main stem. The integration of these three techniques allowed us to obtain quantitative data at the vessel level to improve model parameterization and to go beyond the limits of current approaches in plant ecophysiology.