Coastal freshwater species are monitored in four permanent monitoring sites along the southern coast: in the Archipelago Sea (Brunskär, established in 1991), in the Tvärminne archipelago on the western edge of the Gulf of Finland (2005), off Helsinki (2005), and in the eastern part of the Gulf of Finland (Haapasaari area, 2003). The monitoring programme mainly concerns freshwater fish species living in coastal areas during the warm season and the indicator includes data for four regularly occurring species: European Perch, Roach, Bream and White Bream.

From year 2002 onwards test fishing has been performed using standard multi-mesh gillnets. The Cyprinids included in the indicator are species that thrive in productive, warm waters. An index of the stock biomass, catch per unit effort in weight (CPUE), used in the indicator, can be regarded as an index of the size of the stock as well as of the nutritional conditions and production potential of the area. CPUE herein stands for catch in weight per net per fishing night.

Marine species. The state of the economically most important marine fish stocks in Finland is mainly assessed with age-based models, which use data on catches and sample-based data on catch composition. Annual estimates of the spawning stock biomasses of these fish stocks are made by the working groups of the International Council for the Exploration of the Sea (ICES). The indicator includes stock estimates for Cod, Baltic Herring and Sprat because of their importance and sensitivity to environmental changes.

ICES stock estimates for Cod are made separately for the western and eastern stock, of which the eastern stock ranges eastwards and northwards from Bornholm Island, reaching also Finland's marine area between Kotka and Vaasa. Only the eastern Cod stock is included in the indicator. Stock estimates for the Baltic Herring occurring also in the Finnish territorial waters are made separately for the combined stock in the Baltic Proper and the Gulf of Finland and for one stock in the Gulf of Bothnia (Bothnian Sea region). Both of these are included in the indicator. ICES does not presently provide estimates for the Baltic Herring stock biomass in the Bothnian Bay region. One stock estimate of Sprat, included in the indicator, is made in the whole of Baltic Sea.