Recovery of the fish community of the river Rhine focussed mainly on the return of migratory species, in particular the Atlantic Salmon, Salmo salar, and to a lesser extent on rheophilic fish species. Several limnophilic species that characterize remote parts of the floodplains are, however, also endangered. The status of the fish communities in the floodplains is little known and has been neglected so far. To fill this gap, the present study investigated fish communities in floodplain lakes along the lower River Rhine. To assess how these lakes contribute to fish species richness in the river-floodplain system, the community structure is compared to that in the main channel and to connected backwaters, e.g. side channels, which had been investigated more intensively in recent years. Floodplain lakes with abundant vegetation may have low fish species richness, but they are the only sites with suitable habitats for the reproduction of limnophilic species such as tench Tinea tinca, rudd Scardinius erythrophthalmus and crucian carp Carassius carassius. Limnophilic species in most of these lakes are, however, outnumbered by eurytopic species such as bream Abramis brama, which indicates that the original lateral gradient is truncated with an almost complete loss of 'black fish' habitats in the present active floodplains along the lower Rhine. Floodplain lakes with abundant vegetation should be carefully preserved because they represent original aquatic components that have declined markedly, and they need decades to develop. Preservation of these lakes would enhance the conservation of characteristic limnophilic species. Retention areas outside the present active floodplain - retained as a component of flood risk management - may provide the opportunity to rehabilitate or create floodplain lakes with the suitable spawning and nursery habitats for limnophilic fish. In this way, improved safety may be combined with rehabilitation of floodplain water bodies.