Making a storage compartment water-tight

I have a Tracker Grizzly 1754SC. It has a storage compartment between the
two main seats and one directly behind it. This boat is all aluminum
including the storage compartments. Anytime I get water in the boat either
from rain, swimming, or some water that stays in the boat and is moved
around by trailering or driving the boat, water gets into these two
compartments as they are just an aluminum wall sitting on an aluminum floor.

Here is my question -- any suggestion on how I might seal these seams so to
speak? One compartment has a 1/2" opening on each side on the floor in the
corner. Would silicone caulking do the trick or would that flex and crack
over time with movement of the boat? Ideally, I would like to seal these
and then lay a rubber mat down. Anchors clanking around on an aluminum
painted surface just take off the paint anyway. I have laid a rubber mat
down already that comes up the sides a little bit. It keeps my stuff dry,
but I do end up with water under the mat which I do not want.

Without being water tight, these storage compartments are mostly useless.

Thanks,
Jeff