Natural toxins can be classified according to their origin into biotoxins produced by microorganisms (fungal biotoxins or mycotoxins, algal and bacterial toxins), plant toxins or phytotoxins and animal toxins. Biotoxins are generated to protect organisms from external agents also in the act of predation. Among the different groups, bacterial toxins, mycotoxins and phytotoxins can produce damages in the aquatic environment including water reservoirs, with the consequent potential impact on human health. In the last few decades, a substantial labour of research has been carried out to obtain robust and sensitive analytical methods able to determine their occurrence in the environment. They range from the immunochemistry to analytical methods based on gas chromatography or liquid chromatography coupled to mass spectrometry analysers. In this article, the recent analytical methods for the analysis of biotoxins that can affect freshwater environments, drinking water reservoirs and supply are reviewed.