The purpose of this review is to draw attention to the growing number of secondary metabolites produced by microorganisms in aquatic environments, specially cyanobacteria and marine microalgae. The first group is a producer of major hepatotoxins, neurotoxins and dermatotoxins. Cyanobacteria are responsible for most poisoning events in epicontinental aquatic environments. Eukaryotic microalgae, in marine environments such as diatoms and dinoflagellates, are great producers of a variety of phycotoxins. These syndromes are caused by consumption of contaminated mussels or ciguatera intoxication by consumption of fish (CFP). The current situation demands attention because many events occur and are not notified for important historical studies on seasonal flower blooms. Methodological issues and skilled labor also hinder more precise diagnosis of the blooms. The cooperation between different professionals with different backgrounds as taxonomists, chemists, biologists and environmental engineers is essential for ecotoxicological studies on the risk assessment of these blooms and suggest changes in environmental legislation.