Remove all the water from the fountain. Sprinkle non-iodized salt into the fountain, then scrub with the stiff brush. Rinse the fountain with the garden hose and replace the old water with fresh.
Remove organic debris from the fountain as soon as you notice it. Organic matter from trees, plants and flowers will allow the algae to thrive.
Remove the water fountain tubing and clean with diluted bleach or vinegar to kill the algae residue. Combine 9 parts water with 1 part bleach or 2 parts water with 1 part vinegar.
Pour 1/2 cup of white vinegar into the fountain to discourage algae from forming.
Purchase an algae-blocking solution from a home and garden supply store. The solution will reduce and prevent algae growth if it consistently forms in the fountain. Follow the instructions on the solution to apply it properly.