Blue-green algae are actually a family of photosynthetic bacteria. Cyanobacteria, often called "pond scum", grow in ponds and other fresh water environments but are not consumed by other aquatic life. They are present everywhere on earth, including your garden pond. Some causes of blue-green algae "blooms", are as old as time. Some, we bring about ourselves.
In their book "The Biology and Evolution of Fossil Plants", T.N. and E.L. Taylor place cyanobacteria fossils in the Archaean and Proterozoic Ages (3.8 billion to 543 million years ago). The earliest blue-green algae appear to have been successful because they had warm water and plenty of sunshine. Cyanobacteria thrived in warm seas under a cloudless sky in a nitrogen-rich atmosphere. It combined the nitrogen from the atmosphere with carbon dioxide, phosphates and other nutrients to fix nitrates in plant tissues. The primitive plants then discarded elements---including oxygen---which it could not use. Because blue-green algae had no natural predators, it spread easily throughout the seas and waterways for millions of years, adapting to climates and ecosystems as it went. Whenever it encountered an excess of nitrogen from animal or decaying plant life in a warm, sunny, still waterway, it can "bloom." It enters garden ponds when they are filled, on the scales of fish and on the tongues of predators including foxes, squirrels, even the family cat.
Cyanobacteria are a type of phytoplankton; like other plants, they use chloroplasts to convert sunlight into energy. Today's cyanobacteria take a variety of forms and grow most actively in full sunlight in slow-moving or stagnant warm water. Large populations of fish (which create nitrogen in waste and during population die-off) and heavy concentrations of carbon dioxide in the water cause the explosive growth called blooms. The Inland Lakes Program of Canada reports that, due to cyanobacteria's ability to adjust buoyancy, it may live in bottom silt until it is disturbed by changes in water movement, alterations to the aquatic environment, or a sudden lack of nutrients, all of which can cause it to bloom. As blooms spread, light and air are cut off to the water underneath and dying cyanobacteria produces toxic by-products in the waterways. Its adaptability is a potent example and reason to use sterilized soil in a lily pond or other aquatic garden.
Humans have contributed to the longevity---and adaptation---of cyanobacteria by using nitrogen and phosphate fertilizers on lawns and in agriculture that run off into streams and waterways. The Charles River Watershed Association cites those and other human causes in urban wastewater and runoff containing nitrogen-rich human waste and phosphorus from detergents. Industrial discharges that contain nitrates and phosphorus provide nutrients that can also cause blooms in freshwater rivers, streams and lakes. Many watershed organizations and natural resource agencies advocate the use of "silt shields" to prevent fertilizer runoff and control of nitrate and phosphate-containing fertilizers.