Delineating the characteristics of biosphere-atmosphere exchange in rubber (Hevea brasiliensis Müll. Arg.) plantations, which are rapidly expanding throughout mainland Southeast Asia, is important to understanding the impacts of the land-use change on environmental processes. In attempt to shed new light on the impacts of conversion to rubber, we have conducted eddy flux measurements over a 3-year period in two rubber plantation sites: (1) Som Sanuk, located in northeastern Thailand; and (2) Cambodian Rubber Research Institute (CRRI), located in central Cambodia. Both sites have a distinct dry season. We used a combination of actual evapotranspiration (ET) flux measurements and an inverted version of a simple 2-layer ET model for estimating the mean canopy stomatal conductance (gs). The potential water balance (precipitation (P) − potential evaporation (ET_POT)) for each season (i.e., December–February: DJF, March–May: MAM, June–August: JJA, and September–November: SON) revealed when and how the water use is controlled. In the seasons when actual water balance (P − ET) was negative (DJF and MAM), the deficit was compensated with soil water from the previous season at depths of 0–2 m (Thailand site) and 0–3 m (Cambodia site). At both sites, the reference value of gs (gsref) and the sensitivity of gs to atmospheric demand (m) appeared to be less in DJF and MAM than each in the other two 3-month periods (seasons). On average, in a whole year, m/gsref was less in Thailand (<<0.6) than in Cambodia (near 0.6 for part of the year), suggesting that there was less sufficient stomatal regulation at the Thailand site, where there might be little risk of water stress-induced hydraulic failure because of its higher annual rainfall amount. In comparison, at CRRI where annual P − ET_POT was negative, there was stricter stomatal regulation, preventing excessive xylem cavitation.