Globally, agriculture consumes more than 70% of freshwater resources. A large fraction of the water consumed by agriculture ends up being transpired as water vapor through plant leaves. Predictive modeling of plant/crop soil water uptake under well-watered and drought conditions enables estimation of crop water loss and optimization of irrigation scheduling. 1D models of the soil-plant-atmosphere continuum that estimate crop transpiration do not account for horizontal heterogeneity of the crop canopy. Recently, models that explicitly represent the 3D crop architecture have been developed to account for horizontal heterogeneity effects. However, these models are either built at the leaf cluster scale that does not take the locations of individual leaves into account or ignore the water storage effects in the plants. Here we develop a new plant hydraulic model (v-shoot) that predicts plant water uptake by explicitly representing individual leaves in a three-dimensional canopy architecture. This representation captures the spatio-temporal variations of individual leaf-level processes (photosynthesis and transpiration), which are then integrated at the whole-plant level to predict root water uptake. v-shoot uses 1-D porous media Richards’ equation to model the hydraulics of water flow in plants driven by water potential gradients. The model incorporates the water storage effects in plants. The plant hydraulic structure is modeled as a network of interconnected nodes and links, which are characterized by link (stem) diameter, link (stem segment) length, link (stem segment) hydraulic conductivity, and leaf (boundary conditions) stomatal conductance.