This study measures efficiency of collective floodplain aquaculture enterprises (FPAs) practiced in the floodplains composed of private lands in Bangladesh using data envelopment analysis (DEA). We concentrate on a management system that was initially developed by landowners in the Daudkandi sub-district in 1984. With gradual spread of this management system two important internal variations have emerged in terms of (1) organizational composition that resulted from the investment-based participation of an NGO, and (2) mode of managing aquaculture operation that resulted from leasing out the aquaculture operation instead managing it by themselves in some FPAs. Taking consideration of these two variations, and using four inputs and one output, we measure the technical, scale, mix and overall efficiency of 15 FPAs selected from five districts. While 11 FPAs are technically efficient, only six are overall efficient.On average, NGO-collaborated FPAs (NFPAs) are more efficient (78.27%) than landownersmanaged independent FPAs (IFPAs) (75.96%). However, IFPAs are only found in the Daudkandi region, where there are more efficient IFPAs than NFPAs. On the other hand, while lease-based operations show better average efficiency (79.56%), self-managed operations have more efficient units. We also find that the intensive use of inputs in most older FPAs does not make them more efficient, despite their higher fish yield, than relatively newer FPAs. Given the poverty, food security and nutrition linkage of floodplain aquaculture and continuous attempts to increase fish yield, the FPAs along with development partners and government agencies, should take account of efficiency-related aspects in policies and practice.