The swimming and underwater combat rules are a mess. Falling into water, swimming and fighting while submerged should be especially difficult/deadly to most characters. Generally, the only real penalty that players face is a -2 to hit (which is almost meanigless at higher levels).
There's no way a person who is loaded down with 100's of pounds of combat gear, wearing armour and who actually doesn't know how to swim (why the swim skill can be used untrained is beyond me) should be able to fight against enemies underwater with anything close to normal effectivenss (if at all). Have you ever seen a big muscle bound body builder type (read: high Str and Con) who can't swim jump or fall into water? They sink like a stone! BTW, ever actually try to swim while holding on to something in your hands (like a 2 handed greateaxe). If you are underwater and not braced against anything, you can't actually hit someone with any significant force. Also, thrown weapons are completely ineffective underwater but other ranged weapons simply get a -2 to hit? Modern fire arms lose their effectiveness and force after a few feet through water! How can a x-bow shoot at something from the surface to the bottom of a 100 ft deep lake.
In our campaign we had a Dwarf barbarian load himslef down with rocks in his backpack. Walk underwater and proceed to hack and slash several merfolk to pieces easily. It was ludicrous. Even the players felt bad about it.