A recent ecological study demonstrated a significant association between an increased risk of nonalcoholic liver disease mortality and freshwater cyanobacterial blooms. Moreover, previous epidemiology studies highlighted a relationship between cyanotoxins in drinking water with liver cancer and damage and colorectal cancer. These associations identified cyanobacterial blooms as a global public health and environmental problem, affecting freshwater bodies that are important sources for drinking water, agriculture, and aquafarms. Furthermore, as a result of climate change, it is expected that our freshwater environments will become more favorable for producing harmful blooms that produce various cyanotoxins. Food is an important source of cyanotoxin exposure to humans, but it has been less addressed. This paper synthesizes information from the studies that have investigated cyanotoxins in freshwater and food on a global scale. We also review and summarize the health effects and exposure routes of cyanotoxins and candidates for cyanotoxin treatment methods that can be applied to food.