How to Repair a Pontoon Leak
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Small punctures and pinholes in pontoons might not be immediately noticeable, but can still cause you to take on enough water to cause problems. Eventually, water in the pontoons can cause increased gas consumption due to the extra weight. Steering can also be affected due to the weight distribution becoming uneven. It can also cause the boat to sit too low in the water, and potentially to go under.
Things You'll Need
Clean the area of and around the leak thoroughly.
Sand the area to give the repairing compounds a good surface to stick to. It should not be too smooth, but should not have rough edges.
Fill small punctures with putty, according to its directions.
Allow the putty to cure, then sand it to smooth. For areas with pinholes, mix putty with prepared epoxy sealer to a rollable consistency, and then roll and/or brush it to cover the area.
Wait for the putty and epoxy to dry. Sand it to roughen the surface slightly. Apply a coat of epoxy sealer over the area with a brush and/or roller, and wait for it to dry before proceeding.
Cover the area with a coat of no-sand primer and allow it to dry according to its instructions. The primer and paint for fiberglass hulls works in this instance because you are covering the putty and epoxy, not the metal.
Paint the area with a coat of fiberglass anti-fouling bottom paint. Allow it to dry.Source: ehow.com