Harmful algal blooms in freshwater lakes and rivers, or at estuaries, where rivers flow into the ocean, are caused by cyanobacteria, which are commonly referred to as "blue-green algae", but are in fact prokaryotic bacteria, as opposed to algae which are eukaryotes. Some cyanobacteria, including the widespread genus Microsystis, can produce hazardous cyanotoxins such as microcystins, which are hepatotoxins that harm the liver of mammals. Other types of cyanobacteria can also produce hepatotoxins, as well as neurotoxins, cytotoxins, and endotoxins. Water purification plants may be unable to remove these toxins, leading to increasingly common localised advisories against drinking tap water, as happened in Toledo, Ohio in August 2014.
In August 2021, there were 47 lakes confirmed to have algal blooms in New York State alone. In September 2021, Spokane Countys Environmental Programs issued a HAB alert for Newman Lake following tests showing potentially harmful toxicity levels for cyanobacteria, while in the same month record-high levels of microcystins were reported leading to an extended Do Not Drink advisory for 280 households at Clear Lake, Californias second-largest freshwater lake. Water conditions in Florida, meanwhile, continue to deteriorate under increasing nutrient inflows, causing severe HAB events in both freshwater and marine areas.
HABs also cause harm by blocking the sunlight used by plants and algae to photosynthesise, or by depleting the dissolved oxygen needed by fish and other aquatic animals, which can lead to fish die-offs.  When such oxygen-depleted water covers a large area for an extended period of time, it can become hypoxic or even anoxic; these areas are commonly called dead zones. These dead zones can be the result of numerous different factors ranging from natural phenomenon to deliberate human intervention, and are not just limited to large bodies of fresh water as found in the great lakes, but are also prone to bodies of salt water as well.