But, what can be done?
Weather damage can be prevented of course by adding a bimini canopy top or a hard top. This will protect rain and other weather from hitting the carpet. The best solution is not to get a soft bimini canopy if you go this route. The reason is that the bimini canopy will eventually collapse from weather damage as well. Instead, invest in a hard top like J's Upper Decks. The double deck will add as a weather proof cover, protecting the carpet and the pontoon deck.
Rain is not the only thing to be concerned about. Excessive sun can also cause damage to carpets and wood, especially if the wood is not treated right. Sun can lead to warpping. Having a hard top like an upper deck will keep the sun off the deck and in return, add years to your carpet---and seats!