Understanding of the root zone characteristics and processes in irrigated pecans, an important specialty crop in the southern New Mexico, is a prerequisite to determining patterns of how much and at what rate isolated trees deplete soil moisture before water stress begins to affect its growth and productivity. However, relationship between plant water stress and soil water depletion (SWD) is not investigated thoroughly for irrigated pecans of southern New Mexico. In this study, transient soil water contents, root zone SWD, and midday stem water potential (SWP) were monitored in mature pecan orchards in sandy loam (Site 1) and silty clay loam (Site 2) soils near Las Cruces, New Mexico, on the lower Rio Grande Valley. Corresponding to transient variations of soil water content at different depths, daily SWD varied with soil depth but not spatially. The SWD within the root zone (0–80 cm) was higher in the shallow depths (0–40 cm) where root length density (RLD) was also higher than in the deeper depths (40–80 cm). The SWD at Site 1 was higher compared to Site 2 due to the higher clay content of the latter. The SWD patterns at outside the tree driplines were similar to those under–canopy locations because of similar RLD at the shallow depths. At both orchards, differences in SWP at 2.5, 4.5, and 7.6 m tree heights above the soil surface were evident particularly 10 to 14 days after irrigation. This was due to the stress caused by decreasing soil water contents at different depths, which were generally significantly correlated with SWP. Midday air temperature was as useful as midday atmospheric vapor pressure deficit (VPD) for interpreting SWP. Combined influence of soil water content (0–40 cm) and air temperature on midday SWP was significant at both orchards, which can be used as an adjunct for the clear interpretation of SWP to help refine irrigation scheduling.