Rubber-based (Hevea brasiliensis) agroforestry systems are regarded as the best way to improve the sustainability of rubber monocultures, but few reports have examined water use in such systems. Accordingly, we tested whether interplanting facilitates water utilization of rubber trees using stable isotope (δD, δ(18)O, and δ(13)C) methods and by measuring soil water content (SWC), shoot potential, and leaf C and N concentrations in a Hevea-Flemingia agroforestry system in Xishuangbanna, southwestern China. We detected a big difference in the utilization of different soil layer water between both species in this agroforestry system, as evidenced by the opposite seasonal fluctuations in both δD and δ(18)O in stem water. However, similar predawn shoot potential of rubber trees at both sites demonstrating that the interplanted species did not affect the water requirements of rubber trees greatly. Rubber trees with higher δ(13)C and more stable physiological indexes in this agroforestry system showed higher water use efficiency (WUE) and tolerance ability, and the SWC results suggested this agroforestry is conductive to water conservation. Our results clearly indicated that intercropping legume plants with rubber trees can benefit rubber trees own higher N supply, increase their WUE and better utilize soil water of each soil layer.