Good ideas, everyone.
I'm tempted to let things hold their breath for a number of round equal to their Con score (that's half), because there is a decent chance this might happen to my PC's.
They are basically assaulting the city of Rhest from Red Hand of Doom, except the denizens are different (tanarukk and fiendish troll army). The "fiendlord" at this location is a half-fiend scrag, and the black dragon from RHoD is instead a shadow creature red abishai with an item that lets him breath under water (and a potion of freedom of movement). The lizardfolk have been replaced with Eneko Warrior 4's and Dekanter Goblins (both have Improved Bull Rush).
I think one of my PC's did prepare Water Breathing for investigating the sunken city after the assault, but they do not have it running on anyone at the moment.
There is a decent chance my PC's will have to retreat before they finish the job this time, but they are stubborn and are unlikely to retreat when they should.
They've already taken out six fiendish ice trolls, a scrag, a tanarukk caster, and a half-troll athach, but they are starting to run out of spells, some of their HP's are starting to run low, and the NPC druid is confused and fleeing at the moment. The sentries are gone, but now the big-wigs are stepping in (as well as a few more troll "captains" showing up).
But as I said, there is a decent chance the PC's knock a troll unconscious into the water too. There will shortly be three flying trolls bugging the crap out of the PC's. Two of them will be scrags, so won't care about being under water, but one of them won't be a scrag.