Once harmful algal blooms (HABs) reach a desalination plant, they can cause significant operational issues and potential health concerns for consumers. These issues stem from two factors – first, the algal cells produce organic matter that can cause filter clogging and membrane fouling, and secondly, some cells produce toxic substances or taste and odor compounds. This chapter first explains the mechanisms for cellular release of organic matter, the types of matter that are produced, and the relative contribution of each type of matter to fouling mechanisms. It then describes the wide range of toxins that are produced by HABs, their mode of toxicity, and analytical methods for detecting them. While taste and odor compounds are non-toxic, they are included in this chapter as they can create customer perception issues and distrust in the water supply system.