Fighting underwater involves a lot of new tactics that are not required in regular fighting. Weapons that work well outside of water may work poorly in the water, and vice versa. Here are some of the things you need to do differently when fighting under water:

Strengths of Weapons

Shotgun and Super-shotgun:
These two instant-hit weapons become extremely powerful underwater. Because people move slowly in the water, you can hit with almost every shot.

Nail-gun and Super Nail-gun:
The nail-gun doesn't work as well as the shotgun does underwater, mainly because it's still a relatively weak weapon. It doesn't do a whole lot of damage to begin with, and it's not an instant-hit weapon. It's almost not worth using.

The super nail-gun works awesome underwater. It is actually the weapon of choice for most people when fighting underwater. It does a lot of damage, and though it is not an instant-hit weapon, the enemy moves slow enough that you can hit with most of the nails. A guy with the super nail-gun will beat out a guy with a rocket launcher 75-80% of the time.

The SNG is an awesome weapon underwater

Grenade launcher:
The grenade launcher also works really well underwater. It can fire at a rate a lot faster than a rocket launcher but does the same amount of damage. If you can get close enough, you can pummel anyone underwater. Grenades are usually very tough to hit with because they are too slow… underwater, the slowness of the enemy evens it out.

Rocket launcher:
The rocket launcher, though the most versatile weapon in the game, may not necessarily be best for underwater fighting. You may think that it would be really easy to shoot someone underwater with rockets, because they are moving so slowly, but that is not the case. Generally, you still want to shoot the walls, pillars, and floor if someone is swimming next to them. However, a smart opponent will try to swim in open water, with no walls or pillars next to them for you to it - this will force you to have to hit them squarely in the face… which is why the rocket launcher may not be the best weapon underwater. The most common mistake is that people are shooting the rockets similar to that of when they are fighting someone out of water… meaning they are leading the shots. Underwater, people move slower, so you have to adjust your lead by quite a bit. This takes some getting used to… sometimes too long. I usually prefer switching to the super nail-gun if my enemy has armor underwater.

Lightning gun:
If you fire the lightning gun underwater, be prepared to die along with the rest of the enemies. If you fire the lightning gun underwater, you will do major damage to yourself - exactly 17 health points per cell. (See specs) The lightning gun doesn't act much unlike a lightning would in real life - if you fire an electric bolt in water, you will likely kill yourself and anyone else in the water. However, there are parts of the quake physics that are not similar to that of real life. For example, if you shoot the lightning beam into the water (when you are out of water), nobody in the water will be harmed. If you actually manage to hit someone who's underwater with the shaft from out of water, you will do the same amount of damage as if you were just hitting him with the shaft, out of water. If you are both standing in knee-deep water, you can shaft him and not be discharged. On most occasions, you can even hide behind an underwater pillar (out of the line of sight from the person who's discharging), and avoid being hurt altogether. If you discharge in the water, anyone else in, on, or close to the water that is in your line of sight will receive double the damage you sustained.

If he's got an RL, you can take a chance at a closer spawn and discharge him.

Avoiding Fire From Above

If someone is raining rockets down on you from above water, the best place to avoid the fire is beneath a bridge or platform. It's virtually impossible to hit you from above if you are hiding underneath something… unless, of course, you're next to the ground or a pillar. Stay away from the bottom and walls. Hide behind pillars if it's in between you and the guy who's shooting at you.

Shooting Someone In Water

Use the lightning gun
It can get pretty annoying when someone is floating around in the middle of open water shooting at you while you are above water. It's really hard for you to hit him with rockets because he can swim up and down as well as dodge left and right. I've found the best way to hit someone who's swimming around in water is to use the lightning gun. If he's floating on the surface, the lightning gun will eat him alive. With the shaft, it's really easy to guess where he's going underwater. Give it a try!

The LG is an unparalleled weapon for shooting people at the surface.

Use rockets… but don't aim directly at him
It's pretty hard to shoot someone floating around in water directly in the face, especially when you're not in the water with him. Instead, aim for walls, ceilings, or pillars that may be next to him. Using the same concept as shooting ground, try to kill him with the blast radius and not the rocket itself.

Next: The Artifacts of Quake