Water containing algae have a very less amount of oxygen as the algae consume most of the oxygen dissolved in the water, and thus deprive aquatic plants and oxygen of it, and hence kill them. This results in eventual loss of biodiversity and thus, the balance of nature is broke. This is a kind of pollution it makes happen.
This condition is called- Eutrophication.
Some algae even produce toxins that are harmful to higher forms of life.
P.S.- Algae are formed mostly by addition of chemical fertilisers containing phosphates, which enhance algae growth)