Changing natural landscapes to agricultural land, driven by land demand, have been considered an important driver that limits the ability of landscapes to provide ecosystem services. The decline in ecosystem services in the past are mainly due to anthropogenic farming activities that have been undertaken to satisfy human wellbeing in Africa. Quantifying these declining services over time and space is essential to facilitate sustainable management decisions. In this study, the Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) model was used to quantify and value the ecosystem services in Rwanda from 1990, 2000, and 2010. From the results, while forest cover declined drastically from 61.1% in 1990 and reached 19.9% in 2010, cropland and settlement areas both expanded from 24.7% to 53.4% and from 0.5% to 1.8%, respectively. These variations have resulted in a decrease in total carbon storage from 439.7 Mt to 230.5 Mt in the 20 years, whereas soil export increased from 135 Mt to 712 Mt in 2010. Farmland expansion accelerated the export of nitrogen and phosphorous from 0.9 Mt to 3.1 Mt and 1.0 Mt to 8.4 Mt, respectively. The water yield increased from 2.04 × 109 m3 in 1990 to 2.20 × 109 m3 in 2010. Further tradeoffs analysis reveals that three ecosystem services including water, soil, and nutrient show strong positive correlations with one another, while carbon service appears to have little relationship with the other services. The strategies to manage ecosystem service trade-offs should incorporate farmers’ knowledge and scientific research aimed at increasing agricultural production and resource efficiency in Rwanda. To ensure sustainability, demographic pressures should not be neglected.