In Rwanda, most small-scale hydropower systems are connected to the national grid to supply additional generation capacity. The Rwandan rivers are characterized by low flow-rates and a majority of plants are below 5 MW generation capacity. The purpose of this study is to provide a scientific overview of positive and negative factors affecting the sustainability of small-scale hydropower plants in Rwanda. Based on interviews, field observation, and secondary data for 17 plants, we found that the factors contributing to small-scale hydropower plant sustainability are; favorable regulations and policies supporting sale of electricity to the national grid, sufficient annual rainfall, and suitable topography for run-of-river hydropower plants construction. However, a decrease in river discharge during the dry season affects electricity production while the rainy season is characterized by high levels of sediment and soil erosion. This shortens turbine lifetime, causes unplanned outages, and increases maintenance costs. Further, there is a need to increase local expertise to reduce maintenance cost. Our analysis identifies environmental factors related to the amount and quality of water as the main current problem and potential future threat to the sustainability of small-scale hydropower. The findings are relevant for energy developers, scholars, and policy-makers in Rwanda and East Africa.