The aim of this study was to see the frequency of a certain degree of endangerment of freshwater fish in a certain Natura 2000 area of Croatia and to determine which measures are applied to a particular target species within the Natura 2000 ecological network. Research has shown that there are 35 species of freshwater fish that are also on the Red List of Endangered Species on 60 different habitat types that are part of the Natura 2000 ecological network. According to the results of the analysis, it is evident that species occur more frequently in some areas such as the Delta Neretva and the Middle Stream of the Drava, while in biologically specific areas ( examples of solana) do not occur so often. Given the recording of an individual target species in a given area, it cannot be said that necessarily the species of the richer area has several species that are higher categories of vulnerability according to IUCN. Public institutions responsible for the management of protected areas shall adopt a publicly available Management Plan setting out active measures for the protection of endangered species. Most Public Institutions, according to the management plans adopted so far, implement all recommended protection measures, some implement part, while some have introduced additional protection measures. The analysis showed that the number of active protection measures does not correlate with the number of endangered species on a particular Natura 2000 protected area.