the water shouldn't be there and it's a bad thing, now we've sorted that out, let me think about a cure, if it's an internal moulding it's probaly not connected to the transom too well, if at all, tap all round the drill hole to see if it's live, there should be a dull thud around the outboard bolts and that should be the sound all over.
you need to get it dry for the next bit, but sealing the holes up will just seal the water in, take the bung tube out completely so any water can drain from a bigger hole, this drying is going to take some time, while you're waiting you can redo all the outboard bolts, seal inside and out.
if you can apply heat to the transom do it.
let say you've got it dry, to repair it you will have to drill a hole at the highest point where your transom is live, get a large syringe and pump a hot resin mix down the hole.
it will go without saying but i'll say it anyway, keep all your bungs done up tight when you're in the water, if nothing can get in there will be nothing to come out
i forgot to say, if it's live all over forget everything above, and you don't want to know how it will need to be fix