Biodiversity of European floodplains is seriously threatened mainly due to (1) modifications of river courses such as channelisation or embankments, and (2) changes in traditional agricultural practices (i.e. usually pastures), into intensive production using drainage and fertilisation. A upstream-downstream survey of the Saône floodplain (France) has been done to identify the contribution of habitats to the floodplain biodiversity. Selected taxa were aquatic and terrestrial vegetation, Odonata, Coleoptera, Amphibians, and birds. The taxa were sampled in different habitat types that were: forests, grasslands and aquatic habitats. Tributary confluences with the river and cut-off channels contributed greatly to the floodplain diversity according to their invertebrates and aquatic vegetation communities. The abundance of rare species (benefitting of a national or regional protection status) was the highest in hygrophilous grasslands. Moreover, we demonstrated that diversity of breeding bird communities was correlated with the size of these habitats. We demonstrated also that alluvial forests contributed to maintain some particular species as Middle-spotted Woodpecker (Dendrocopus medius), while new plantations were colonized by openland bird communities sensible to the edge effect. Grassland fragmentation for agriculture appeared to be a major cause in biodiversity loss. Any alteration of the floodplain dynamics must be avoided to preserve the present diversity of riverine wetlands.