•Longitudinal and lateral occurrence traits for 163 lampreys and fishes were developed.•Species-specific Fish Region and Floodplain Fish indices were derived.•Macro-scale indicators show deviation of fish assemblages from reference state.•The indices are broadly applicable and independent of regional species pools. This study aims to complement existing fish-based assessment approaches by classifying European lampreys and fish species according to their probability of occurrence in six different longitudinal river regions and five types of floodplain water bodies under unimpaired conditions. The main objective was to provide for the first time harmonized occurrence traits for European lampreys and fishes in both longitudinal and lateral dimensions of floodplain river systems in a Fish Region Index (FRI) and Floodplain Fish Index (FFI), respectively. Altogether 163 lamprey and fish species established in European rivers have been scored according to their longitudinal and lateral occurrence probabilities. The species-specific Fish Region and Floodplain Fish indices and their variances inform about species’ occurrence probabilities, dispersal traits and potential species inventories of different river regions and floodplain waters. The final scores allow identifying characteristic fish assemblages, i.e. a set of type-specific species for the different longitudinal river regions and lateral floodplain water bodies. The species-specific index values and variances serve to calculate summary metrics for the total fish assemblage (FRItotal and FFItotal) as macro-scale indicators for the deviation of the total fish assemblage from a reference state. The resulting index values indicate degradation as well as rehabilitation success at the level of fish assemblages, i.e. at an ecologically relevant macro-scale. Both species-specific and total assemblage indices are directly comparable among all biogeographic regions of Europe independent of the local species pool. As such, the indices serve as assemblage indicators for the fish-based assessment of the ecological status of water body types and river regions in floodplain river systems, which are required in particular for the assessment of large floodplain rivers.