Seems like every time I have to repair a seaplane, when I peek under the covering there's an infestation of mildew. Today, I opened up a previously undamaged wing that's only been on a seaplane for 2-3 weeks, and it's got a load of mildew in it.

What can I treat the balsa with before construction to prevent mildew? (It must not prevent the covering/glue from bonding to the balsa)

Kilz prevents mildew but I don't Know if it is suitable for covering.

After i fly my sea plane i take the wing off and let totally dry. Have never had a mildew problem. Also after losing two planes in the lake i started taking the Batt. And RX out of the plastic bag and let dry. Havnt had a problem since.

You could coat the whole thing with epoxy (heehee)

I've never had mildew but I've seen it on others. Before I cover something I plan on flying off the water, I spray the whole framework with a light coat of polyurethane (from a can). I wonder if that helps. Anyone know?

You might also try venting the whole structure as you build your next plane. I believe mildew starts from trapped moisture which can't evaporate thus creating an ideal environment for the mildew fungus to start growing. I also agree with tpstory that spraying the entire structure with polyurethane will help seal up the wood and help preserve the structure.
I always disassemble my planes so they can breath when I'm not using them. I'm sure boat builders, especially those in coastal areas have a few tricks to prevent this problem.
My current project is a twin engine, scaled-up Aqua-Star for two 25's. I hope to keep this plane for many years so preservation is a priority topic.
Lets keep this thread alive because I for one would also like to have a few tips on this matter.
Peter