This would be a pretty huge change for the game, considering how many firefights end up taking place in the water, but it would go a long way in terms of balancing the current weapons under water and adding something new/fun to the game. Also, obviously, real flintlocks don't work under water at all.
This is kind of the fun compromise. If you were to greatly reduce the effective range of bullets under water, you would eliminate the obvious supremacy of sniper/pistol under water(you can shoot people from miles away, they can't move and they have no cover). It would force underwater combat to happen close range.
Adding a portable harpoon gun as an actual weapon would serve two purposes: one, give players a mid-range option for under water combat. two, give players a tool to defend from deep swimmers with kegs. There's two variations I can see with this: Either roped or ropeless.
Ropeless would just serve as a long distance gun, that specifically excels under water. It would still be useable on land but would basically just be a flintlock with a slightly longer reload time.
Roped would allow you to pull people to you or pull yourself to them. This could be used under water to pull enemies close for combat or prevent enemies from escaping. Or, if they have a keg, just stealing right out of their hands.