This paper presents economic analysis, viability and trade-off issues for small-scale (family) inland capture fisheries in three fishing communities, each representing a distinct floodplain characteristic in Cambodia. The average net profits of family fishing was US$12 and US$4.6 per trip during the open (October to May) and close (June to September) seasons, respectively; but real profit—deducting the cost for family labour from net profit—was only US$4.5 and US$1.6 during the open and close seasons, respectively. The return from family fishing varied greatly across sites surveyed, depending on the quality of the fishing grounds, hydro-ecology settings, local institutions, and socio-economic factors. The high degree of seasonality, the spatial variation of returns and costs of capture fisheries suggest interdependence of fishing activities with basin-level water allocation policies, and also related trade-off in the fisheries sector with water allocation and water resources management policies. There is also now an urgent need for synergy of the various rural development efforts with that of fisheries policies in the Mekong River Basin.