The pastoral systems of Eastern Africa have been affected by the alternated incidence of recurrent drought and flood for the last decades, aggravating poverty and local conflicts. We have introduced an innovation to convert floods to productive use using water spreading weirs (WSW) as an entry point to capture and spread the torrential flood emerging in the neighboring highlands into rangelands and crop fields of low-lying pastoral systems in Afar, Ethiopia. The productivity and landscape feature have changed from an abandoned field to a productive landscape within 3 years of intervention. The flood patterns and sediment loads created at least four different crop management zones and productivity levels. Based on moisture and nutrient regimes, we developed land suitability maps for integrating crops and forages fitting to specific niches. The outcome was a fast recovery of landscapes, with 150% biomass yield increment, increased access to dry season feed and food. These positive outcomes could be attributed to the proper design of weirs, joint planning and execution between pastoralists, researchers and development agents, identification and availing best-fitting varieties for each management zone and developing simple GIS-based parcel level maps to guide development agents and pastoralists. The major ‘agents’ were community leaders (‘Kedoh Abbobati’) who keenly debated potential benefits and drawbacks of innovations, enforced customary rules and byelaw and suggested changes in approaches and choices of interventions. In general, an innovation system approach helped to create local confidence, attract attention of government institutions and helped local actors to identify investment areas, develop implementation strategies to increase productivity, define changes as it occurs and minimize conflicts between competing communities. However, the risk of de facto use of a plot of communal land translating into long-term occupation and ownership may be impacting a communal territory and social cohesion that was subject to other collective choice customary rules.