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Finnish lakes (187 888 lakes larger than 5 ares) and archipelago have a very high recreational and touristic value, and surface water is often used for the production of drinking water. While many shallow lakes have been affected by anthropogenic eutrophication especially in the agricultural areas of southern Finland, water monitoring and protection programmes have shown positive development during the last few years.

Intensive research on toxic cyanobacteria has been carried out in Helsinki and Turku since the 1980s. The results show that cyanobacterial and cyanotoxin diversity in Finnish lakes is high, and tens of microcystins, anatoxin-a, saxitoxins and cylindrospermopsin as well as other bioactive compounds have been characterised from Finnish freshwater cyanobacteria. The Baltic Sea suffers from intensive blooms of nodularin-producing Nodularia spumigena.