If you can determine when the water is entering the bilge, you will narrow down the causes. Yes, you can seal all the seams, deck plates, deck panels but if you think that rain water is leaking down, nothing beats a garden hose. Just flood the deck and check every now and then for bilge water. Start aft and work forward. The anchor locker lid and windlass are common places for water entry.
If water is accumulating only when running or while sitting at the slip, you have a whole different issue.