Well first of all it looks like you have a beautiful pool! Normally I would have recommend two things for your situation long term 1) they should have let the horizontal stone run under the vertical piece to not cause this problem in the first place. 2) anywhere you have submerged tile I would use an epoxy grout. (about 10 times more expensive than regular grout) Because you have what looks like natural stone weir, you would need to test to make sure that they will not stain the stone!
Short term you should make sure that this area has a high quality sealer applied. Even if your contractor sealed the weir (most would NOT) it has been 3 years outdoors I would apply/reapply, use a high quality sealer like stonetech bulletproof sealer. You can try to caulk this area but there are actually very few sealants that are allowed to be submerged. This decision come down to appearance vs performance. You can try a high quality silicone sealant like Dow Corning 795 that will give you many color options but will not be recommended by the manufacture for this use or you can use a product like 3M 5200, but it only comes in 4 colors. :-(
NO MATER WHAT you do apply sealer first! you will have to dry the tile out first which sucks but it will probably help prevent this problem in the future.
Good Luck!