If I understand this right, if he is in water, he has Stealth, but line of fire is only blocked if there is hindering terrain in the way? The water itself does not put him "in stealth"?

Assuming that SP description is accurate (I don't have my card in front of me right now), that is correct. Water terrain is clear terrain for LOF and Stealth has no effect on Water all by its lonesome.

Another question:
If Atlantean Warrior uses Charge (starting in water), but exits the water. Does he lose Charge? Can he still attack( keeping charge for the action), or does leaving the water make the attack not possible?
If yes then: Charging out of water ,using stealth. Can an opponents P.C.er draw line of fire to Atlantean Warrior (during the attack) if hindering terrain is in the way?

I think if he begins the action in water, then yes, he can charge, even if he charges out of the water.

I guess I'm recalling the discussion on pounce , when they changed how objects worked.
I know pounce is a feat, but, being in water is sort of a prerequisite for having Charge and Stealth through his SP. Once it's out of water, it no longer meets the requirements of having either of those powers.

Outside of taking damage during a flurry attack (and similar), I can't think of a character losing a power in the middle of an action.

I know actions can become invalid (range combat attack vs. wildcarded stealth)-and you're allowed a different action. Or (say) Charge vs. a successful Shapechange- you've moved, but the free attack is lost (if no other adjacent figures).

I could be wrong, but my guess is that they goofed and intended to give the Atlanean Warrior the same special ability as Aqualad, but add charge into the mix.

FROM THE DEPTHS: Aqualad can use Charge. When Aqualad occupies water terrain, any line of fire drawn to him is treated as if it crosses blocking terrain.

Of course with the way they've worded it, until there's an errata correcting this, we have to play with a character that has a useless stealth or am I missing something? Is there a way to use stealth in the water with the wording of the current power?

Stand on an object that's in the water?

Or the line of fire crosses some hindering terrain between the attacker and the water.

I see it as the Atlantean being waist deep, so that you can't see them if there's a gumball machine in the way.

It will work too if you play a Deep Shadow : all non blocking terrain (incluiding water terrain) will become hindering for LOF purposes, and all your Atlantean Warriors in water will vanish... Freaky !

Cap'

You can put Smoke Cloud tokens on water terrain too.
[insert Deep Purple reference of your choice here]