AbstractTropical rainforests are rich in tree species and comprise complex canopy structures. Transpiration by forest trees is a major hydrological flux which contributes to climate regulation. We explored the role of forest canopy structure on tree transpiration in a tropical rainforest on Sumatra, Indonesia. Drone‐based photogrammetry and the structure from motion technique were used to compute high‐resolution 3D point clouds and derive forest and tree structural variables. Transpiration of differently sized and vertically positioned trees was assessed with sap flux measurements. Per‐tree transpiration rates increased linearly with several variables related to crown dimension and were further enhanced by top‐heavy crown shape, dense leafage and increasing canopy openness as assessed with the gap light index. Under given environmental conditions, the two variables crown volume and top‐heaviness explained 74% of the observed variance in per‐tree transpiration. Transpiration rates per unit crown dimension were highest for small crowns, decreased non‐linearly with increasing crown dimension and were little affected by other analysed structural variables. Our study underlines the potential of 3D point cloud analyses for accurately determining the structure of complex forest canopies and thus better understanding and predicting transpiration rates of differently positioned trees.