Soil Physics & Hydrology pecan [(Carya illinoinensis (Wangenh.) k. koch] is an important specialty crop in New Mexico. This research quantifies soil water and soil nitrate-nitrogen (NO 3-N) (mg L −1 of soil) variations with depth, root NO 3-N (kg ha −1) uptake, and NO 3-N (kg ha −1) balance for the 100-cm soil profile during two growing seasons in a flood-irrigated pecan orchard. Nitrate-nitrogen was determined six times during the growing seasons of 2015 and 2016. The HYDrUs-1D model was used to optimize the water flow parameters using measured volumetric soil water content (q). Model calibration and validation for NO 3-N included the optimization of reaction parameters for nitrification and denitrification of each soil layer. The results showed that the model simulated q well (0.44 £ d [index of agreement] £ 0.73) at different depths during both calibration (2009) and validation (2010) periods. generally, HYDrUs-1D simulated soil profile NO 3-N concentrations that were correlated with measurements at all depths during both years. Total root NO 3-N uptake showed a significant increase of 72% in 2016 compared with 2015. The NO 3-N balance showed that ?40% of applied NO 3-N per year was denitrified, which was the main contributor to the NO 3-N loss from the soil profile during both years. Nitrate-nitrogen leaching below the soil profile was 32 and 26% of applied NO 3-N in 2015 and 2016, respectively. The fertigation rate was much higher than the plant demand during both years, and it should be decreased to reduce NO 3-N losses.