You have a tall order there, trying to make a wood floor waterproof. The only way I see it can be done is to repair/replace the subfloor and I prefer the plywood route, I would make it Underlayment grade Tounge&groove OSB. As you install the subfloor, glue it to the joists, glue the end joints and the T&G which will help to waterproof a little. That type of OSB is very tolerant of moisture for a while.
Ultimately the waterproofing has to be on top of the wood flooring, using a heavy duty sealer and several coats of Porch And Floor enamel. If the water is stopped anywhere else it will lay there and soften the wood, causing quick rot.