The perfect storm. That is the term used by Gerald C. Nelson to describe the triple challenge of increasing food production while adapting to climate change and reducing the environmental impact of agricultural systems. Nowadays, conventional farming systems are showing some limitations, such as low resources use efficiency and poor ecosystems servicesthatappear to be associated to the loss of plant diversity and perenniality in crop rotations.In addition, water, the most importantyield limiting factor worldwide, will increasingly restrict food production in the future dueto rainfall shortage andincrease in human consumption.In such context, perennial crops,with denser and deeper root system could use resources indeep soil layers that are logically inaccessible to crops with shallower rootsystem.The goal of this thesis was therefore to investigate the root growth and water uptake capacity ofintermediate wheatgrass (Kernza®) and alfalfa, two deep rooted perennial crops, under field conditions and at great soil depth (i.e. 1.0-2.5 m).Maintaininghydraulic continuity along the soil-plant-atmosphere continuumis aprerequisite for deep water uptake. At the plant level, hydraulic conductivity dependson complex anatomicaland physiological processes among whichthe root system constitutes the second largest resistance to water flow.Therefore, in depth characterisation of root and xylem anatomy was done to understand the hydraulic properties of the crop root systems, with a focus on their evolution with soildepth. Crops were grown inthefield, rhizoboxes, mesocosmsand solution culture to take into account the variability of root type and soil depth as well as growing environment.For both crops, axial hydraulic conductance decreased with soil depth and along individual root segment. Alfalfa roots had greater axial hydraulic conductance in comparison to intermediate wheatgrass roots, especially at depth. Root and xylem anatomy were highly variable across crop species, root types and growing environments. In parallel, a combination of imaging and sensor technology, stable isotope techniques and a modelling approach was used to study root growth and water uptake under field conditions during the 2018-2019 seasons. Both crops presented roots down to 2.0 m soil depth that were active in terms of water uptake. Alfalfa had greater root length at depth and absorbed twice as much water below 1 m soil depth, than intermediate wheatgrass. For both crops, model simulations predicted that water uptake in deep soil layers (i.e. 1.5 –2.0 m) increase (i.e.>30%) under dry conditions.This thesis brings insights into the understudied fieldof root growth and water uptakeat great soil depth.Particular efforts were put in understanding the environmental and agricultural contexts in whichdeep root growth, deep water uptakeand the development of perennial cropping systems would be possible and favourable.