The phenomenon of blue-green algae blooms in the Baltic and the surrounding freshwater bodies has been known since several years. Recently these blooms have increased. The negative effects of this phenomenon concern not only environ-ment but also pose epidemiological threats because some blue-green algae produce toxins. The presence of potential toxic blue-green algae species in the Gulf of Gda?sk as well in the whole southern Baltic has been noticed for almost hundred years. In the recent years, when water temperature reached more than 18?C, the rapid growth of Nodularia spumigena has been observed. In the year 1994, the huge bloom with toxic features of this species has been noticed. With less intensity such a bloom appeared also in 1996. Since several years Anabaena flos-aquae blooms in the Vistula Lagoon and Microcystis flos-aquae in many lakes in the Kashubian Lakeland.