So my issue here is that I can't find specific rules for the Vortex ability that water elementals have. What it says in the rules is
A water elemental can create a whirlpool as a standard action, at will. This ability functions identically to the whirlwind special attack, but can only form underwater and cannot leave the water.
Now, my issue is how to translate from air and flying, to water and swimming. Let's start at the top:
If the creature has a fly speed, it can continue to fly at that same speed while in whirlwind form; otherwise it gains a fly speed equal to its base land speed (average maneuverability) while in whirlwind form.
I assume this would instead translate into Swim Speed, instead of Fly speed. The question here is more if it can move beneath the surface, which I think is reasonable but - again - I'm here because I'm not 100% sure. And if it's at the surface, do people have to make swim checks to stay afloat, and what DC would it be? Personally I think stormy water makes sense, with a DC of 20.
A creature that can fly is allowed a Reflex save each round to escape the whirlwind.
Now obviously this makes little sense for a whirlpool in water, it'd be more of a swimming issue, right? However, anyone can swim, so if you let anyone roll a Reflex Save every turn then not only is it much more situational than the whirlwind special attack, but also easier to escape. But there are fewer creatures with a swimming speed than people who can fly, meaning that if you limit it to creatures with a swimming speed then almost no one can escape it once in it. That might however balance out the fact that it's so situational. Should people instead make a swim check? And should it maybe be either a swim check or a reflex save, the lower of the two if you don't have a swim speed, and the higher of the two if you do have a swim speed? Or maybe a reflex save is limited to those with ranks or a certain amount of ranks in swim? I'm just spitballing here, I'd like to hear you guys' input.
If the whirlwind’s base touches the ground, it creates a swirling cloud of debris.
This I assume just works the same, except it would be the bottom of the ocean/lake/body of water.
There's always the 3rd-Party rules about whirlpools, maybe one can incorporate them into this.
To me it seems logical that, where you replace "fly" with "swim", it specifically means those with a swim speed. I mean, if people are being tossed around by an air elemental's vortex, ranks in Fly aren't enough to escape. One has to actually have a fly speed.
As for keeping one's head above water (while you get tossed around and beaten to death in a vortex you can't escape), I think the DC 20 (stormy water) is reasonable.
The Water Elemental's vortex should be comparably dangerous to the Air Elemental's. After all they are the same DC.
The Water's vortex is more limited in where is can be effective, and the "swirly cloud of debris" is also less relevant because it only hampers the vision of underwater combatants. Ships, flying creatures, and those on the surface wouldn't be affected by the debris. The only real tradeoff is that the water's vortex has the additional threat of drowning.
In other news... I just made up a Sorcerer build, Water Elemental Bloodline.
Combining Elemental Body VI and Seamantle is very mean. You can make a 30' whirlpool anywhere, thanks to Seamantle's 30' column of water.
Double-move, sweep through 240'x15' of the battlefield and everyone in your path (of appropriate size) gets pulled into the watery cyclone of doom.
If you cast Fire Shield before that, everyone also takes fire or cold damage too. It's pretty vicious.