Variable rate application in precision agriculture requires an exact quantification of the variability within the orchard. A sensor fusion framework integrating visible‐light optical imagery with infrared thermal data acquired by an uncrewed aerial vehicle was employed to demonstrate the potential of drone-based data for quantifying the spatial influence of windbreaks in a citrus orchard in the Western Cape of South Africa. Sensor fusion employed a 3D reconstruction derived from structure-from-motion techniques to delineate individual citrus tree crowns. Following georectification of both datasets, these crown delineations were integrated with the thermal imagery. Modelling techniques such as Voronoi growing space analyses and generalised additive regression models were then applied to quantify the spatial effect of the windbreak structure on the surface temperature and the crown volume of the citrus trees. The main results show the dominant impact of the distance to the windbreak, which led to increased crown surface temperatures in proximal trees and smaller crowns as a consequence. Also, the height difference of the windbreak to the citrus trees had an effect, however, a much weaker one. All in all, the newly developed methodology showed a promising way to analyse the variability within the orchard as a base for a more precise management.