Spatio-temporal effects of herbicide including 3-(3,4 dichlorophenyl)-1,1-dimethylurea (DCMU) on a whole melon (Cucumis melo L.) plant were three-dimensionally monitored using combined range and chlorophyll a fluorescence imaging. The herbicide was treated to soil in a pot and the changes in chlorophyll a fluorescence images of the plant were captured over time. The time series of chlorophyll fluorescence images were combined with 3D polygon model of the whole plant taken by a high-resolution portable scanning lidar. From the produced 3D chlorophyll fluorescence model, it was observed that the increase of chlorophyll fluorescence appeared along veins of leaves and gradually expanded to mesophylls. In addition, it was found by detailed analysis of the images that the invisible herbicide injury on the mature leaves occurred earlier and more severely than on the young and old leaves. The distance from veins, whole leaf area and leaf inclination influenced the extent of the injury within the leaves. These results indicated difference in uptake of herbicide in the plant from soil depends on structural parameters of leaves and the microenvironments as well as leaf age. The findings showed that 3D monitoring using combined range and chlorophyll a fluorescence imaging can be utilised for understanding spatio-temporal changes of herbicide effects on a whole plant.