Stormwater runoff poses serious environmental problems and public health issues in Rwanda, a tropical country that is increasingly suffering from severe floods, landslides, soil erosion and water pollution. Using the WetSpa Extension model, this study assessed the changes in rainfall runoff depth in Rwanda from 1990 to 2016 in response to precipitation and land use changes. Our results show that Rwanda has experienced a significant conversion of natural forest and grassland to cropland and built-up areas. During the period 1990-2016, 7090.02 km(2) (64.5%) and 1715.26 km(2) (32.1%) of forest and grassland covers were lost, respectively, while the cropland and built-up areas increased by 135.3% (8503.75 km(2)) and 304.3% (355.02 km(2)), respectively. According to our estimates, the land use change effect resulted in a national mean runoff depth increase of 2.33 mm/year (0.38%). Although precipitation change affected the inter-annual fluctuation of runoff, the long-term trend of runoff was dominated by land use change. The top five districts that experienced the annual runoff depth increase (all >3.8 mm/year) are Rubavu, Nyabihu, Ngororero, Gakenke, and Musanze. Their annual runoff depths increased at a rate of >3.8 mm/year during the past 27 years, due to severe deforestation (ranging from 62% to 85%) and cropland expansion (ranging from 123% to 293%). These areas require high priority in runoff control using terracing in croplands and rainwater harvesting systems such as dam/reservoirs, percolation tanks, storage tanks, etc. The wet season runoff was three times higher than the dry season runoff in Rwanda; appropriate rainwater management and reservation could provide valuable irrigation water for the dry season or drought years (late rainfall onsets or early rainfall cessations). It was estimated that a reservation of 30.5% (3.99 km(3)) of the runoff in the wet season could meet the cropland irrigation water gap during the dry season in 2016.