Irrigated agriculture, particularly small-scale irrigation (SSI), is a mainstay for sustainable livelihoods in the developing world. In Ethiopia, SSI sustainability is threatened mainly due to excessive sedimentation. Stakeholders’ perceptions of the causes of sedimentation and how they sustain SSI under excessive sedimentation conditions were investigated in two SSI schemes in Ethiopia. A participatory rapid diagnosis and action planning was implemented, consisting of a literature review, participatory rural appraisal, and semi-structured interviews. Results show that farmers slightly differed in perception of excessive sedimentation drivers. Farmers reported design problems as the main cause of excessive sedimentation (64%), followed by poor operation and maintenance (O and M) practices (21%) and external factors (15%). In contrast, 62% of the interviewed engineers indicated erosion and irrigation technologies as the main causes of excessive sedimentation, while few reported poor design (13%). In addition to an intensive desilting campaign, farmers delayed the start of the irrigation season to avoid the intake of highly sedimented water. Local social capital and knowledge appeared to be more important than formal knowledge and blue-print institutions for dealing with sedimentation problems. Well-organized structure and extra time devoted by famers were vital for SSI sustainability. Integration of the farmers’ knowledge with that of the engineers could yield more effective ways to deal with sedimentation problems.