The fish-based farming system encompasses mixed fishing/farming households that derive from 30 to 50 per cent of their income from fisheries and engage in a wider livelihood portfolio including forestry, livestock production, hunting and gathering. It covers a range of ecosystems, climatic zones and sociopolitical contexts. The majority of rural households in the system engage in small-scale fishing, especially young men using canoes and gill nets, but women and children also operate on foot. Fisheries can still be regulated by traditional institutions, but the trends are towards ineffective, state-based regulation or free-for-all situations. Externally financed, larger-scale operations at greater distances from the farm are on the rise. Fishery productivity is largely dependent on the flood pulse linked to seasonal rainfall patterns. Deforestation, land degradation and weather extremes are creating unfavourable, sharper and shorter flood peaks. River regulation by dams decreases system extent and productivity. Trends are towards declining recession agriculture, pasture production and fish reproduction. Large-scale irrigation systems tend to replace the system and exclude its original beneficiaries. Understanding of the system’s functional requirements and its wide-ranging benefits is scanty in both government and development agencies, and thus some pessimism about its future is justified. Emphasis has been on extracting more from the system through industrialisation and upscaling, including for export, but failures are rife. Less attention has been directed to maintaining and enhancing system productivity through ecosystem management interventions, and facilitating the small-scale fisher-farmer’s operations through co-management. The absence of an enabling environment and heavy local taxation favours self-sufficiency rather than marketing. Maintenance of the structural and functional integrity of the wetland ecosystems should be a key focus, especially maintaining the flood pulse, including through managed flood releases from dams. Co-management, based on traditional governance systems, has a better chance of effectively banning destructive techniques and safeguarding nursery areas and reproductive seasons. There is a need for jointly analysed and agreed interventions, more flexible mesh-size regulations suited to local conditions, irrigation systems designed to add to the natural system, and maintenance of input-effective recession agriculture and other flood-based biodiversity, ecosystems and livelihoods. Given climate change uncertainties, planning must include wide error margins for floodplain infrastructure. Aquaculture production is rapidly expanding. The introduction of inappropriate species should be avoided. Emphasis should be on fish that are low in the food chain (e.g. tilapia) and also on the preservation of the natural systems and existing water bodies. Small-scale testing, incremental technological improvements and household level roll-out may be the more sustainable and equitable approach. Culture of the ubiquitous, oil-rich and nutritious catfish Clarias gariepinus, which survives in almost any habitat and is the perfect fish to be smoked, offers opportunities using simple village ponds seeded from the wild. Much can be learned from projects initiated by non-governmental organisations, but interventions should preferably be embedded in local government and operate over medium-scale timeframes. Support through holistic (non-sectoral) and non-dogmatic rural extension workers with a thorough understanding of the local context should be prioritised. Options for governance reform determined via multi-stakeholder dialogue and considering evidence, livelihood security, human rights and cross-sectoral and cross-scale interactions need to be explored.