Flood-based Agricultural Systems (FAS), which rely on temporary floods, provide livelihoods for nearly 50 million smallholder farmers across water-stressed African basins. This paper analyses the impact of externally driven agricultural production and productivity improvement interventions in FAS, taking the Ethiopian Fogera floodplain as a case study. Ostroms’ Governing the Commons Principles were used as analytical framework. Field data was gathered through focus group discussions and interviews with 266 farmers and pastoralists, and 10 local administration staff, while the AquaCrop model was used to simulate maize yield under varied floodwater management and farming practices. The interventions in the Fogera floodplain replaced vital maize and teff food crops with high-return upstream rice cultivation. It has characteristics similar to other interventions across Africa: 1) inadequate integration of local agricultural water management practices; 2) narrow focus on short-term economic gains and insufficient attention to long-term sustainability of livelihoods and environmental issues; and 3) lack of detailed ex-ante analysis of basin-wide consequences – it failed to prioritize the needs of downstream vegetable producers and pastoralists using shallow wells. The intervention missed several low-cost opportunities, including the establishment of rules to protect downstream water rights; the construction of gabion-strengthened on-farm structures to efficiently distribute floods or raised brick-walls to reinforce shallow wells; and the implementation of measures for improved soil fertility and weed management. The study establishes that these missed opportunities could have enhanced livelihoods by doubling rice yield to 6 tons/ha; increased teff and maize harvests by one-third, to 3 and 5 tons/ha respectively; and mitigated 25% vegetable yield loss and 40% reduction in grazing land. These opportunities could have also produced environmental benefits, including reduced soil moisture and fertility depletion. Lessons from the Fogera floodplain on making interventions cost-effective and considering basin-wide livelihood impacts are relevant to FAS globally.