The extensive flooded land associated with the Three Gorges Reservoir, poses a great social and environmental challenge, yet it is a potential valuable land and sociological resource for resolving human-land conflicts in the surrounding communities. Controversies arose over use or non-use of such land among local communities and authorities; and different management strategies were adopted. We compared two representative ecosystems, Wuyang Bay in small-scale agricultural use through opportunistic farming, and Baijiaxi Bay in a state of natural succession, and learned the challenges-cum-opportunities regarding sustainability through an agro-ecological perspective. We integrated the plant diversity, water quality improvement, market production services and people's attitudes to obtain a holistic evaluation of the socio-ecological and economic benefits delivered by two bays. Significant differences were found: Wuyang Bay performed much better than Baijiaxi Bay in terms of plant diversity maintenance and people's acceptance. Regarding the concerns about impacts on reservoir water, Wuyang Bay has lower TN, and NH4-N concentrations than Baijiaxi Bay. This may be because of the decomposition of a large amount of naturally grown-drowned vegetation in Baijiaxi Bay. Emergy analysis showed that the economic efficiency of Wuyang Bay is better than other similar systems given its limited growing season. However, this is at the expense of the environment through chemical fertilisers and pesticides seeping into the reservoir waters. Strictly speaking, Wuyang Bay cannot be counted as a sustainable agro-ecosystem although it hints at many practical merits, such as integrating natural landscape elements in fields, and employing multiple crops in spatial and temporal patterns. Our study offers newinsights into the impacts of world's largest reservoir construction on the livelihoods of nearby communities on a small scale and the possible solutions. With the use or-not contradiction, the government should offer appropriate policies and technical support to incentivise farmers to a more sustainable, multi-functional living landscape. (C) 2018 Elsevier B.V. All rights reserved.