Pontoon boats are often left outside in the rain and humidity, thus increasing the chance of moss growth on the synthetic carpeting. Most commercial moss killers are actually toxic to marine life and plants, so you cannot spray them or wash them off while the boat is near any type of water way. Attempt the least toxic moss removal method first, although it is always a good idea to clean your pontoon carpeting on dry land to avoid contaminating the water.
Park or tow your pontoon boat to a good place for moss removal, such as a driveway. Make sure no plants will be harmed by any moss removal compounds. Have a garden hose with access to clean water handy for rinsing the boat.
Fill a clean plastic spray bottle with vinegar. Use regular white household vinegar, because this product is strong enough to kill moss, but does not need to be diluted with water. Vinegar is safe to use on the synthetic pontoon carpeting, but does need to be rinsed off after using.
Spray the vinegar directly on all mossy spots. Allow the vinegar to sit for about 10 minutes and penetrate the moss completely. The longer the vinegar sits, the more likely it will thoroughly kill the moss.
Scrub the mossy spots with the scrub brush. It should lift right off the carpeting, but will leave behind a messy residue. If your boat has a lot of moss you may want to sweep up the moss pieces before rinsing, to avoid spraying moss debris all over the driveway.
Spray and rinse water from the garden hose onto the scrubbed areas. You may want to do this between scrubbing, to keep the area clean and monitor your progress. If possible, attach a pressure washing nozzle on to your hose to get the carpet thoroughly rinsed.
Dry the pontoon boat and carpeting outside in the sunshine. If any stubborn moss spots persist, you can try to spot clean them with a few drops of bleach added to tap water in a spray bottle, but this could fade or slightly damage the carpeting. Rinse well afterward.