Phytotoxins are secondary metabolites that plants produce to defend themselves against diseases, herbivores, insects, biotic and abiotic stress conditions, pests, etc. They exhibit huge diversity in their structures, chemical composition, and toxicity. They have been extricated from both terrestrial and aquatic sources and can be categorized into numerous classes such as terpenes, alkaloids, glycosides, phenolics, cyanotoxins, coumarins, tannins, quinones, and many more. In plant kingdom, the generation of secondary metabolites is primarily an extensive phenomenon of protection from potential predators and unfavourable circumstances. However, aside from shielding plant from various environmental stressors, these plant secondary metabolites have a wide range of applications in various other fields. They can be utilized as biopesticides and herbicides, in medicine and healthcare as anti-inflammatory, antiviral, antimicrobial, and antitumour resources. They have been utilized in vaccines and drug development as well. Aside from these beneficial properties, in terms of mobility, persistence, and toxicity, many of these phytotoxins might have certain characteristics similar to anthropogenic micropollutants. Keeping in view their immense applicability, the present book chapter summarizes the various kinds, aquatic sources, and applications of phytotoxins along with their role as micropollutants.