If you do not have any coatings at all on the bottom of the boat, we suggest to sand the pontoons with 80 grit and then apply Tuff Stuff High Build Epoxy. It is a water tight barrier coat designed for use under the waterline and with aluminum hulls. Tuff Stuff will insure that you protect the aluminum from corrosion, and also aid in the adhesion of the antifouling paint. Use 2 coats. You can apply the 2nd coat within a couple of hours of the first coat. See detailed instructions at “How to Apply Marine Epoxy Primer”.
After you apply Tuff Stuff marine epoxy primer on hull, be sure to use an aluminum safe antifouling paint. The bottom paint needs to be applied the same day as the Tuff Stuff marine epoxy primer. Antifoulants in general are designed to repel hard growth. For soft growth you should have an additional biocide that help with the algae. Smart Solution is an excellent antifoul for aluminum pontoons used in salt water as well as Mission Bay for fresh or salt water.
WARNING: You should only use an aluminum safe antifouling like Mission Bay or Smart Solution. Using any other type of copper based antifouling could severely damage your pontoons and will cause corrosion, pitting and eventually holes in your pontoon boat.
You can add Bioboost to the Smart Solution antifouling paint which will further help with algae. Check out the video link below for these products applied to pontoons. These can be brushed, sprayed, or rolled. The Bioboost should simply be added to Smart Solution or Mission Bay right before use. If you already have coating(s) on the hull, pressure wash, sand with 80 grit, and then apply one of the aluminum safe antifouling paints.
How to Video: Aluminum Pontoon Antifouling Paint Application