Reservoir-based irrigation schemes (RBISs) have been developed to minimize the adverse effects of moisture stress and improve the livelihoods of smallholder farmers in semi-arid regions. However, many RBISs perform below expectations. A multistage expert elicitation approach and an indicator-based Sustainability Assessment of Food and Agriculture System (SAFA) framework were used to identify sustainability challenges and management interventions. The expert elicitation was used to address the sustainability issues of RBISs at the regional scale, whereas the SAFA was used to evaluate the sustainability of the four RBISs. Adapting holistic approaches is advantageous for covering broader sustainability dimensions and including all irrigation system components. The expert elicitation approach fills the data limitation gap in prioritizing management practices to address sustainability challenges. The implementation of prioritized management practices should consider local socio-economic and environmental aspects. The SAFA has limitations in taking into account the effects of erosion in hotspot areas. The expert elicitation approach has a limited ability to consider views from stakeholders outside the biophysical boundary and the fate of schemes after sedimentation of the reservoirs. A combination of both approaches could result in a better implementation strategy for identified management practices to ensure the sustainability of RBISs.