Great introduction, now for the fix. The top deck and hull come together  
beneath the rub rail. The fix is to remove the rubber part of the rub rail. This  
will expose either the plastic or aluminum (depending on year) base of the 
rub  rail. It is most likely pop riveted in place. Drill out the heads of the 
rivets  and you will be able to remove the base.
You will notice the base piece has a lip which curls under the joint. Clean  
the area of any old sealant and dirt and I would recommend a final cleaning 
with  a good solvent. Once the area is clean and dry, I would recommend sealing 
it  with a one part polyurethane sealant like a product called NP1. It is 
available  at most roofing supply company's and Sherwin William stores have their 
own  brand. If you can't find it, anything that is a one part polyurethane 
will  suffice. It is sticky like nothing else and remains pliable for twelve 
years in  extreme weather conditions. Great for using on boats.
Instead of applying it to the seam with a trailing motion, you will apply  it 
with the nozzle facing forward, forcing sealant into the joint. I found  
cutting the tip off flat further down and then notching it with a V was an easy  
way to apply it. Place a small bead on the lip of the base and reinstall  with 
pop rivets. You will find the old pop rivets inside the cabin for some time  
to come.
Now for the real question. I am going to assume that you have actually  
sailed the boat and buried the rail enough to force water in the hull in this  
manner. Rain water is not likely to enter the boat through this joint. If it is,  
then you have a problem with a completely different fix.
I hope this helps. If you need further assistance, please ask.
 
Rrrrrrrrrrummy