Copied from the link above:
On leaking storage boxes: The leak is from the top somewhere on most cases. You will notice that the boxes hold water, thus they are not leaking from the lower section. They must be leaking from the top side. And DO NOT drill into the hull trying to drain a box. This is a MAJOR MISTAKE>!!!
1. Check the locks to be sure that the rubber o-rings are sealing on the locks if you have the T-Handle style of Perko. If you have the older D ring style, the lock itself is a major source of water leakage into the boxes.
On the locks itself, you can use plumbers grease to lower seepage into the box through the lock itself.
2. Check the lock mounting to be sure they are tight in that location.
3. There are small neoprene and aluminum washers on all of the hardware screwed into the lips or various mounting hardware. Check for leakage at all of the #10 machine screws. Tighten them and check the washers for leakage. They can come loose and also work loose and leak in any drain channels they are supposed to flew into and seal. This is worse on older boats.
4. The interior light string is riveted to the box lip, and those can work loose and while seldom leaking there check it in any case.
5. Then check the trim seal around hte box. The boats in the more recent time have a molded trim seal together, though older boats have a glued on bubble strip on the trim. Also check the trim joint for an issue there at the seam. The seam location may also be improper. Then check that the trim seal is all on the box lip.
6. The TEST: Once you have checked everything, then you can test the boxes for leakage. In order to do this, elevate the nose on the boat slightly, pitching the decks to the rear for water fall off (drainage).
Take a brown paper of some sort, like a body paper (body Shop mask off), or brown grocery sacks cut out and laid flat in the boxes. Cover the entire lower section of the boxes. Be sure you have all of the opening with brown paper under them.
Latch all of the compartments making sure the locks are covered or the T handles are in their grooves with o -rings in place.
Now take a garbage can with about 15 to 25 gallons of water in the can itself. Totally inundate the deck area with the water in one deluge of a dousing. Yes dump it all at once!
Allow the water to drain from the deck, and in a few minutes, open the lids and check the paper fo water spotting or indications of water trails in the paper.
Be sure to just let the water drain off naturally first.
7. Another source of water in the boxes is any water left in the bilge, which runs up the bow of the boat when you stop, and pressurizes itself into the bow area by the front trolling recess, shooting into the under deck bow area through the triangular drain channel for the bow.
Once it shoots to the bow, it splashes into the nose and finds its way around to the rod boxes.
The center storage’s should be totally sealed including the top edges. The only major source of water for these is those listed above. You can put your head in the boxes and look up to check the upper seal in the glass.
Hope this helps!
BCB