We developed a soil-vegetation-atmosphere transfer (SVAT) model applicable to simulating CO₂ and H₂O fluxes from the canopies of rubber plantations, which are characterized by distinct canopy clumping produced by regular spacing of plantation trees. Rubber (Hevea brasiliensis Müll. Arg.) plantations, which are rapidly expanding into both climatically optimal and sub-optimal environments throughout mainland Southeast Asia, potentially change the partitioning of water, energy, and carbon at multiple scales, compared with traditional land covers that are being replaced. Describing the biosphere–atmosphere exchange in rubber plantations via SVAT modeling is, therefore, important to understanding the impacts on environmental processes. The regular spacing of plantation trees creates a peculiar canopy structure that is not well represented in most SVAT models, which generally assume a non-uniform spacing of vegetation. Herein we develop a SVAT model applicable to a rubber plantation and an evaluation method for its canopy structure, and examine how the peculiar canopy structure of rubber plantations affects canopy CO₂ and H₂O exchanges. Model results are compared with measurements collected at a field site in central Cambodia. Our findings suggest that it is crucial to account for intensive canopy clumping in order to reproduce observed rubber plantation fluxes. These results suggest a potentially optimal spacing of rubber trees to produce high primary productivity and water use efficiency.