Consult your fountain's instruction manual, if provided, to check for any special tips or cautions regarding cleaning the fountain. Some fountain materials require special care.
Unplug the fountain pump and drain the water. Smaller fountains can simply be turned over and dumped into the grass or toilet, while larger ones usually have drain plugs.
Wipe the fountain down with a cleaning rag, concentrating on areas where algae has built up. Most algae growth will wipe off easily.
Use white vinegar and an old soft-bristled toothbrush to clean tough algae growth. White vinegar is mild enough to be used on nearly any fountain surface, and will remove most stains and discolored spots.
Use pipe cleaners to clear algae buildup out of the holes that the water pours out of at the top of some types of fountains. Gently insert them into the holes, twist around, and pull them out.
Rinse the fountain well, refill the water and plug it back in.
Place the fountain in a spot where it doesn't receive direct sunlight, if possible. This will cut down on the incidence of algae blooms.
Prevent future algae growth with fountain algaecide. There are several natural options available that are gentle yet effective. These water treatments are economical as well: Since you only need to use a few drops per gallon of water in the fountain weekly, a small bottle can last a long time.