The cyanobacteria or cyanoprokaryota, formerly green–blue algae, (Class: Cyanophyta) is a cosmopolitan and diverse group of organisms, living in freshwater and seawater, running or quiet waters, in a benthic or planktonic manner. Some cellular strains from several cyanobacteria genera have toxigenic properties. Cyanobacteria produce potent toxins with a broad chemical nature and effects, like alkaloids and peptides with acute hepatotoxic, cytotoxic, neurotoxic and gastrointestinal disturbances, and respiratory and allergic reactions. Although other algal groups also produce toxins, cyanobacteria are responsible for most poisoning events in freshwater. Toxic cyanobacteria blooms are a major concern for reservoir managers, and corporations that manage supplies of drinking water usually implement complex monitoring programmes to prevent and predict these toxic events, but this type of programme for monitoring toxic blooms is seldom implemented in Nature Reserves. Based on almost a decade of experience after the implementation of the early warning network for preventing mass wildlife mortalities as a consequence of cyanobacteria bloom in Doñana National Park (SW Spain), we propose some guidelines to design a monitoring programme to detect cyanobacteria blooms. Additionally to environmental variables measuring such as pH, temperature, nutrient load, etc., we suggest later identifying and counting the cyanobacteria at the laboratory, as well measuring toxin concentration. Based on all these information gathered, both in the field and at the laboratory, we could establish the blooming risk level linked to certain threshold. Each proposed risk level has associated a panoply of monitoring and management measurements to surveillance the blooming and to avoid wildlife deaths.