Freshwater fishes represent about one quarter of the worlds vertebrates. They are also the most species-rich group amongst European vertebrates.

Biogeographers usually classify freshwater fishes according to their tolerance to salt water. Primary division families are those whose members are strictly intolerant of salt water, at present and historically. Secondary division families are those whose members now live in freshwater but are able, or supposedly once were able, to tolerate seawater for a short period. In addition to these categories that apply to entire families, many species that occur in freshwaters do actually belong to primarily marine families:

• diadromous species are species that migrate between fresh and seawater at different periods of their life, either to spawn in the sea (catadromous) or in freshwater (anadromous);
• vicarious species are non-diadromous, strictly freshwater species of primarily marine families;
• sporadic species are species that seem to be indifferent to salinity (i.e. euryhaline) and usually occur in estuaries;
• accidental species are defined as normally marine species that are very occasionally caught in inland waters; their occurrence is not predictable and there are usually only a few records of the species in freshwaters.

The majority of Europe's freshwater fish species belong to one of the following two taxonomic groups;

• the warm-water adapted Cypriniforms, such as carps, chubs, dace and loaches, which have their highest level of species diversity in the southern and temperate parts of Europe;
• the Salmoniforms, such as salmon, trout, grayling and whitefish, which are most abundant and diverse in mountainous regions and in northern Europe.

Both groups are well known for including many local endemics at species and subspecies levels. A third major group are the Percimorphs. Even though rather species-poor, they often occupy a key ecological role in freshwater ecosystems.

All species of freshwater fishes recorded from European freshwater waters were included in the assessment. Marine migrants and species of brackish waters were also included if they regularly enter freshwater habitats. In total 531 species were assessed, 382 of which are present in the 27 member states of the European Union.