This work presents a detailed analysis of cyanotoxins (secondary metabolites) produced by toxic cyanobacteria (blue-green algae) and known for their harmful effects on humans, animals, and plants. Particular attention was paid to defining the different types of cyanotoxins (hepatotoxins, neurotoxins, dermatotoxins, etc.), their types and modes of action, as well as their ecological implications for agricultural products, human health, and the environment. The various techniques and analyses (biological, physicochemical, and molecular) most commonly used in detection and biomonitoring were also presented and discussed. Case studies were presented and discussed to demonstrate the practical aspects of the methodologies used. The data set could serve as a reference not only for the scientific community, but also for managers of aquatic environments affected by toxic cyanobacteria.