This study assesses the impact of climate change on hydrological processes under rice intensification in three headwater inland valley watersheds characterized by different land conditions. The Soil and Water Assessment Tool was used to simulate the combined impacts of two land use scenarios defined as converting 25% and 75% of lowland savannah into rice cultivation, and two climate scenarios (A1B and B1) of the Intergovernmental Panel on Climate Change Special Report on Emissions Scenarios. The simulations were performed based on the traditional and the rainfed-bunded rice cultivation systems and analyzed up to the year 2049 with a special focus on the period of 2030-2049. Compared to land use, climate change impact on hydrological processes was overwhelming at all watersheds. The watersheds with a high portion of cultivated areas are more sensitive to changes in climate resulting in a decrease of water yield of up to 50% (145 mm). Bunded fields cause a rise in surface runoff projected to be up to 28% (18 mm) in their lowlands, while processes were insignificantly affected at the vegetation dominated-watershed. Analyzing three watersheds instead of one as is usually done provides further insight into the natural variability and therefore gives more evidence of possible future processes and management strategies.