Commercial agricultural production of orchards is based on water and fertilizer applications. Over-application and orchard spatial variability lead to water and nitrogen (N) losses through leaching and environmental damage. This work introduces a novel advanced method to quantify N and water leaching at the orchard scale by combining soil monitoring, unmanned aerial vehicle (UAV) imagery to estimate tree size, leaf N and canopy content, and water flow and N transport models. Four neighboring commercial orange orchards were selected, and 48 representative trees were instrumented with suction cups and tensiometers at a depth of 90 cm. The physical properties of the soil profiles in the vicinity of each tree were determined. During 2019–2021, UAV structure-from-motion (SfM) photogrammetry was used to classify the tree sizes into small, medium, and big categories. Soil porewater extraction and soil matric potential measurements were conducted every three weeks, while leaf N contents (LNC) were determined through bimonthly leaf tissue sampling. The LNC, N leaching, soil water state, and N use efficiency (NUE) (the ratio between the mass of plant N uptake and the mass of N applied per area) were strongly related to tree size classification. Results of the calibrated hydrological model illustrated that the 'big' trees exhibited minimal N leaching due to higher transpiration compared to the other tree size categories. An NUE map was established using the calibrated model and field measurements, demonstrating that soil spatial variability minimally affected N leaching compared to tree size distribution. The presented holistic approach can be used to identify N-leaching hotspots, improve orchard scale NUE estimates, and promote sustainable agricultural management practices.