The Water-Aliens are able to manipulate water and can even create 100ft tidal waves and then freeze them in place. Compared to something that complex, imagine how simple it would be for them to manipulate the water in a human body if they wanted to.
They repaired the damage done to Jammer's brain by the oxygen imbalance.
They keep Lindsey alive long enough for her to be revivied aboard the Deep Core.
They keep Bud alive and functional on his descent, and guide his intuition to help him cut the right wire.
And, as stated above, they bring the crew to the surface and prevent them from suffering The Bends on the way up.