In JTAS #22 Marcus Rowland wrote up some rules for underwater combat in Classic Traveller. Basically what he says is that unless the weapon has been specially modified for underwater use (or was designed that way from the start) it will be of little or no use in underwater combat. The only exceptions are space combat missiles (which are still greatly reduced in range) and meson guns.
Of the personal weapons described in Book 2/Book 4 I would say that the rocket-powered weapons (snub pistol, accelerator rifle, RAM grenade launcher) would be the most use when unmodified, and even they would be greatly reduced in range. Laser weapons would work, but again be badly cut in range, and a laser's hitting power would also fall off rapidly underwater.
If a projectile weapon was modified to work underwater (I'm not sure how, one idea that comes to mind would be have a blast of high-pressure air that pushes the water out of the barrel right before the gun fires) then you could fire it, but you'll still lose range and damage quickly because of the resistance of the water.
So underwater combat is short-ranged unless you have weapons designed for underwater combat, and then you have the trouble of finding your target, for which you need special underwater sensors. Such sensors are mentioned in Rowland's JTAS article. Basically radar and other electromagnetic sensors won't work very well, you need sonar or high-tech sensors like mass detectors/densiometers.