Ray Clark's epoxy suggestion reminds me of a wooden skiff that I restored back in 1977 that I had bought for $30 since it had been submerged for at least several months in an estuary and was covered in oyster shells. After months of grinding and sanding I poured fiberglass resin into all areas...
A waterproof and durable but expensive alternative to plywood is COOSA Board. It comes in various thicknesses up to 2" thick. It's essentially a hard, very light but strong, essentially waterproof, urethane foam core material. board widely used to replace rotted wood transoms and planks like the...