Seafarer's Handbook (Fantasy Flight) has good underwater combat rules in it. If you like a more somewhat scientific take on things, both MEG's The Deep and Bastion's Into the Blue are good supplements to have as they work well in tandem together.
Another nod for Seafarer's Handbook. Also, if you know someone with a good 2e collection, take a look at the Monstrous Arcana book for the Sauhaugin. Sea Devils or something like that.
Classic Play: the Book of the Sea (Mongoose) has a load of stuff on underwater adventuring, magic and creatures. (I wrote it, so if you've any questions or want to know how it would cover problems in your campaign, ask away ).
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