While there is increasing evidence concerning the detrimental effects of expanding rubber plantations on biodiversity and local water balances, their implications on regional hydrology remain uncertain. We studied a mesoscale watershed (100 km2) in the Xishuangbanna prefecture, Yunnan Province, China. The influence of land-cover change on streamflow recorded since 1992 was isolated from that of rainfall variability using cross-simulation matrices produced with the monthly lumped conceptual water balance model GR2M. Our results indicate a statistically significant reduction in wet and dry season streamflow from 1992 to 2002, followed by an insignificant increase until 2006. Analysis of satellite images from 1992, 2002, 2007, and 2010 shows a gradual increase in the areal percentage of rubber tree plantations at the watershed scale. However, there were marked heterogeneities in land conversions (between forest, farmland, grassland, and rubber tree plantations), and in their distribution across elevations and slopes, among the studied periods. Possible effects of this heterogeneity on hydrological processes, controlled mainly by infiltration and evapotranspiration, are discussed in light of the hydrological changes observed over the study period. We suggest pathways to improve the eco-hydrological functionalities of rubber tree plantations, particularly those enhancing dry-season base flow, and recommend how to monitor them.