Abstract The assessment of changes in the population spread of individual ichthyofauna species (lampreys and fishes) as well as the identification of unfavourable impacts is the necessary prerequisite for the correct selection of corrective measures. The river network in the Czech Republic belongs to the three sea-drainage areas (North Sea, Baltic Sea, and Black Sea). The species composition of the original ichthyofauna and the extent of the threat to some species differs in the individual sea-drainage areas. The original ichthyofauna in the Czech Republic consists of 4 lamprey species and 55 fish species. Out of this, only one lamprey species and 31 fish species originate in all three sea-drainage areas. There are 37 fish species considered as the original ones in the North Sea drainage area, there of 4 species are EX, 1 species EW, and 11 species (29.7%) are threatened. In the Baltic Sea drainage area, there are 4 species EX, 1 species EW, and 8 species (22.8%) threatened out of the total 35 assessed species. Out of 49 species in the Black Sea drainage area, there are 4 species EX and 23 species (46.9 %) threatened. The most important reasons considered as the causes of the disappearance or reduction in the presence of some fishes are the water pollution, adjustments to water flow beds, the limitation of floods in alluvial areas, the permanent river basin fragmentation, and the spread of invasive species. Out of these factors, the only positive change has been noticed in the pronounced decrease in water flow pollution after 1990. Angling is also considered as the set of targeted bio manipulation which purposefully and often one-sidedly influences fish populations for the benefit of species being interesting for the angling sport.