There are rules in the SRD for the penalties for fighting underwater without freedom of movement.
Generally, though, its nasty position for the party, because they take a bunch of minuses and have to make loads of checks, while their probably water-adapted foes do not.
My suggestion is to read and reread those aquatic combat rules, (and any others you also intend to use) and then to write them on an index card or print them out for reference during the game. (Or sticky-note the page in the DMG) By the end of the adventure, everyone should be a master of aquatic combat rules.
Also remember visibility will be an issue - water may be clear, but its only lit so deep from sunlight, and torches can't be used. (Though there are other ways) Plus, dirt and grime could be stirred up with movement, totally obscuring vision.
The idea does have some interesting encounter possibilities. Try mixing non-standard tactics into the combats for more memorable encounters. (Try and disable/dispel water breathing abilities? Poison that saps Strength, and therefore, Swim? Swarms of unnatural predatory fish could be a hazard) Don't make them too harsh, but try to pick challenges that wouldn't be possible on land.
For more ideas, WotC has an environmental book "Stormwrack" that has other supplemental rules for aquatic combat. (Things like hazards, monsters and spells, rules for pressure damage and the like, etc)
Interesting Idea - Since combat can and will be 3 dimensional underwater, try having attackers with ranged weapons (special underwater throwing weapons, spells, or just plain rocks lobbed by many creatures) attack from high up (30-50') for an interesting encounter. The characters wishing to reach them will do much better without armor, but getting close with out armor will probably spell their doom. This could make for some interesting tactical choices: Attack head on with little defenses, or find another way around at the expense of possibly falling into an (even worse) ambush.
EDIT: Easy references:
http://www.d20srd.org/srd/skills/swim.htm - Swiming Skill rules
http://www.d20srd.org/srd/environment.htm#waterDangers - Basic water rules
http://www.d20srd.org/srd/wilderness.htm#aquaticTerrain - Underwater combat rules