This chapter begins by examining the types of harmful algal blooms (HABs) observed in freshwater systems. The term harmful algal bloom refers to a host of both cyanobacterial and noncyanobacterial species that create health problems for humans and animals. In 2008, the Interagency Working Group on Harmful Algal Blooms, Hypoxia, and Human Health developed the Scientific Assessment of Freshwater Algal Blooms [1], which reviewed current understanding of HAB occurrence in the United States. A discussion of the frequency of occurrence and the geographical distribution of HABs in freshwater systems is also presented in this chapter to establish the magnitude of the problem in the United States and globally. Once an understanding of the frequency and occurrence of HABs is developed, this chapter focuses on exploring the physical, chemical, and biological factors that are important in the formation of HABs and those factors that control the persistence and die-off of blooms. The ultimate impact of HABs on people and animals also depends on the expression and release of toxin from HAB species. This chapter summarizes the main factors that inuence the “toxin quota” in HAB species, as well as the factors that inuence toxin release in freshwater systems.