Drain the fountain. You can remove the water by hand using a cup, or for quicker removal use a wet/dry vacuum.
Clean the pump and its tubing and spouts using a toothbrush and a mixture of ½ cup vinegar and 1 gallon of warm water. Rinse clean and allow the parts to dry completely.
Use a toothbrush to scrub the fountain bowl with a vinegar and water mixture. Combine ½ cup vinegar with 1 gallon of water. Rinse the fountain with water and allow the fountain to dry completely.
Clean algae stains with a mixture of dish soap and water. Use a toothbrush to scrub the stains, and rinse with warm water and allow the areas to dry completely.
Soak any rocks or loose parts on the fountain in vinegar. Vinegar helps stop the growth of algae.