Massive accumulations of cyanobacteria (a.k.a. “blue-green algae”), known as freshwater harmful algal blooms (FHABs), are a common global occurrence in water bodies used for recreational purposes and drinking water purification. Bloom prevalence is increased due to anthropogenic changes in land use, agricultural activity, and climate change. These photosynthetic bacteria produce a range of toxic secondary metabolites that affect animals and humans at both chronic and acute dosages. Children are especially at risk because of their lower body weight, behavior, and toxic effects on development. Here we review common FHAB toxins, related clinical symptoms, acceptable concentrations in drinking water, case studies of children’s and young adults’ exposures to FHAB toxins through drinking water and food, methods of environmental and clinical detection in potential cases of intoxication, and best practices for FHAB prevention.