With a growing concern for the water conservation and efficient water use of irrigated pecan orchards in the lower Rio Grande valley of southern New Mexico, evaluation of deep percolation and its effects on root zone soil water dynamics in flood-irrigated mature pecan orchards is essential for the understanding of soil–plant–atmosphere water relations, groundwater recharge and irrigation management. Therefore, objectives of this study were to: (1) characterize deep percolation below the root zone based on soil water balance method and Root Zone Water Quality Model (RZWQM2) simulations in pecan orchards grown under sandy loam and silty clay loam soils, (2) evaluate effects of deep percolation on root zone soil water dynamics and groundwater table levels, and (3) evaluate effects of root zone soil water dynamics and groundwater table levels on evapotranspiration (transpiration and evaporation). During the period from April 2009 to December 2010, transient soil water content and soil temperature at different soil depths up to 160 cm and 40 cm, respectively; root zone soil water depletion at under–canopy and outside the tree dripline locations; groundwater table level; leaf area index; stem water potential at different tree heights above the soil surface; and meteorological data were monitored in two mature pecan orchards grown under sandy loam and silty clay loam soils near Las Cruces, New Mexico. Soil physical, hydrological and thermal properties at both pecan orchards were determined. We are attempting to apply RZWQM2 to evaluate deep percolation and its effects on root zone soil water dynamics in both pecan orchards. The research will provide quantitative estimates of deep percolation below the root zone in pecan orchards grown under sandy loam and silty clay loam soils, as well as its effects on root zone soil water variations and groundwater table levels, and evapotranspiration.