The Game Mastery section for Environment is a good place to look first.
Aquatic Terrain
The Stealth and Detection section is a good point to study, since if you can't see your target it's harder to attack them.
The Underwater Combat table should answer most questions about attack and damage modifiers for various actions.
The basic answer will be that slashing and bludgeoning attacks are at a -2 to attack and only deal half damage. Ranged attacks will be at a -2 to attack for every 5 feet of water they pass through (in addition to normal range penalties.) Thrown weapons are pretty much useless.
Obviously, you can (and should) make obvious calls for specific attacks that would likely be hindered in normal underwater use (ie. not with freedom of movement or such). A sling, for instance, is not technically a thrown weapon but you could declare it to be unusable underwater due to the need to spin it quickly around and generate sufficient speed. Another example might be a certain creature's claw attack. While claws typically do both piercing and slashing damage, you might fairly rule a claw attack to be at a -2 attack penalty due to the way the attack is made but with no damage penalty because it is still piercing. Of course, that should only apply to non-aquatic creatures in that case, since aquatic ones should be assumed to be acclimated and evolved for such things.
