Mix one cup ammonia, ¼ cup baking soda and ½ cup distilled white vinegar until the baking soda dissolves.
Pour the mixture into one gallon of water. The water will dilute it enough so that it does not damage your porcelain or fiberglass toilet.
Pour the solution into a spray bottle.
Shut off your home's water.
Flush the toilet as much as needed to remove all of the water from the tank and from the bowl. Some toilets may not drain completely. If this is the case, use a disposable cup to bail out the water in the tank.
Spray the cleaning solution on the entire surface of the toilet. Focus on areas that have visible fungus growth so that the growth is completely soaked.
Let the solution sit for at least 20 minutes. Give the solution time to loosen the fungus' grip on the surface of the toilet so that it will be easier to scrub away.
Scrub the fungus off the toilet with a toilet scrubber.
Wipe down any exterior surfaces with a clean cloth.
Turn the water back on.
Flush the toilet until you've rinsed the entire inside of the toilet.