Quantitative information about the spatial and temporal patterns of compensatory root water uptake (RWU) in flood-irrigated pecan orchard is limited. We evaluated spatio-temporal compensated and uncompensated RWU patterns of mature pecan tree in a silty clay loam orchard using the HYDRUS (2D/3D) model. HYDRUS (2D/3D) simulations, which agreed well with measured water contents and temperatures at different soil depths and horizontal distances from the tree trunk, suggested that while both compensated and uncompensated RWU varied with soil depth they did not do so laterally because of similar spatial vertical distributions of root length density (RLD) for the under-canopy and the tree canopy dripline locations. Considering compensated RWU resulted in an increase in actual transpiration by 8%, and a decrease in evaporation and drainage by 5% and 50%, respectively, during a growing season. Simulated transpiration and relative transpiration (a ratio between actual and potential transpiration) values were correlated with measured transpiration and plant-based water stress indicators (stem and leaf water potentials), respectively. Overall, our results of the spatio-temporal compensatory RWU provide support to use HYDRUS (2D/3D) as a tool for managing efficient water use of pecan. © 2013 American Society of Civil Engineers. ASCE/AUGUST 2013.