Cyanobacteria are photosynthetic organisms found in aquatic and terrestrial biotopes and ecosystems throughout the world. Marine and freshwater cyanobacteria have been extensively studied due to the toxic hazards that some of them create and biotechnological interest. In contrast, the cyanobacteria of brackish waters have been less studied despite being able to form toxic blooms like their freshwater and marine counterparts. We review the occurrence, diversity and toxicity of cyanobacteria species in the brackish waters of Europe, mainly estuaries and brackish environments of the Atlantic Ocean and the Mediterranean and Baltic Seas. The dominant cyanobacteria belong mainly to the planktonic genera Nodularia, Aphanizomenon, Microcystis and Anabaena, but also the benthic forms of Anabaena and Phormidium. Most genera from brackish waters are reported to be hepatotoxin producers (microcystin and nodularin). However, anatoxin-a and other bioactive compounds (e.g. apoptogens) can also be found and are produced exclusively by benthic forms. Nodularin is the best-characterized brackish-water cyanotoxin, being primarily produced by N. spumigena. Data are presented on cyanotoxin production, accumulation, and potential food chain transfer, with a particular focus on nodularin, which induces multiple effects on food-chain dynamics. Microcystins and anatoxin-a are also considered. Potential risks to animals and humans from cyanotoxin exposure are discussed, although reports of animal poisoning by brackish-water toxic cyanobacteria are scarce and no cases of human intoxication are yet known.