It depends on what they are. ...

It depends on what they are. Some cyanobacteria produce toxins that can harm livestock (and humans who drink the water). The big blooms of algae occur because of nutrient run off into the water body. The problem becomes that when the algae die, and decompose, the decomposition reduces oxygen in the water leading to fish kills. dead/decomposing fish will make it worse (LOTS of nutrients) Run off into water bodies is not easy to control. Sustainable agricultural practices such as reducing fertilizer use/not over fertilizing in proximity to the water can help in the long term. The biomass can be removed. (often the bad blooms of cyanobacteria float on the surface of the water. Be aware that the material can cause rashes and skin irritation, depending on what kind of algae it is). It can be dried and pelletized to burn for fuel needs. It can be anaerobically digested to produce biogas. It can be composted for use as a soil amendment (be aware the biomass can concentrate metals and that is good to test before applying to soil where food is grown). Check out Oilgae.com, and algaeindustrymagazine.com as these sites (and many others) have information on these uses of biomass.