In applied ecophysiological studies related to global warming and water scarcity, the water status of fruit is of increasing importance in the context of fresh food production. In the present work, a fruit water stress index (FWSI) is introduced for close analysis of the relationship between fruit and air temperatures. A sensor system consisting of light detection and ranging (LiDAR) sensor and thermal camera was employed to remotely analyze apple trees (Malus x domestica Borkh. "Gala") by means of 3D point clouds. After geometric calibration of the sensor system, the temperature values were assigned in the corresponding 3D point cloud to reconstruct a thermal point cloud of the entire canopy. The annotated points belonging to the fruit were segmented, providing annotated fruit point clouds. Such estimated 3D distribution of fruit surface temperature (T Est) was highly correlated to manually recorded reference temperature (r 2 = 0.93). As methodological innovation, based on T Est, the fruit water stress index (FWSI Est) was introduced, potentially providing more detailed information on the fruit compared to the crop water stress index of whole canopy obtained from established 2D thermal imaging. FWSI Est showed low error when compared to manual reference data. Considering in total 302 apples, FWSI Est increased during the season. Additional diel measurements on 50 apples, each at 6 measurements per day (in total 600 apples), were performed in the commercial harvest window. FWSI Est calculated with air temperature plus 5 °C appeared as diel hysteresis. Such diurnal changes of FWSI Est and those throughout fruit development provide a new ecophysiological tool aimed at 3D spatiotemporal fruit analysis and particularly more efficient, capturing more samples, insight in the specific requests of crop management.