Karst terrain (carbonate rocks) covers a vast land of 0.446 million km2 in southwest China. Water yield and carbonate rocks weathering in this region have been receiving increased attention due to a large-scale forest recovery. Using both hydrological measurements and forest inventories from 1986 to 2007 in the Houzhai karst basin (HKB), we analyzed the responses of water yield and dissolved inorganic carbon (DIC) export to forest recovery in southwest China. With implementation of both the Natural Forest Conservation Program (NFCP) and the Conversion of Farmland to Forests Program (CFFP), the fraction of forest area in HKB was increased from near zero to 18.9% during the study period, but the ratio of total water yield (surface and underground) to precipitation varied very little over the annual period, neither in wet season nor in dry season. By contrast, the concentration of DIC in water, especially in the surface water had a pronounced increase during the study period, with an increase of 0.53 and 0.25 g C m−3 yr−1 for surface water and underground water, respectively. As a result, total annual DIC export at mean annual rainfall significantly increased from the low to high forest area stage. This increase was largely driven by surface water during the wet season, presumably being related to biological activity. It was concluded that forest recovery in HKB had no significant effect on water yield, but resulted in more carbon dioxide (CO2) dissolved in karst water accompanying with carbon uptake by forests. Our results suggested that implementations of both NFCP and CFFP had no shifted water yield regimes in southwest China; instead, they might have alleviated global climate change by increasing carbon uptake through combined biological processes and carbonate rocks weathering. Copyright © 2013 John Wiley & Sons, Ltd.