There are several meanings behind water - one that comes to mind for many people is a cleansing or rebirth, in line with the Christian concept of baptism. The character will go under water (may or may not include drowning) and come back up a new person.
This can also happen in the crossing of the water. If you want to go classic literature, think Huck Finn - life on the raft and on the river is serene, a recreation of the Garden of Eden almost, with the river providing everything that Huck and Jim need. However, when they enter land, there is chaos and deception, etc.
In Greek mythology, people had to pay to cross the River Styx in order to move on with their lives. In more modern time, it's not an accident that Harry Potter first enters Hogwarts via a boat.
The sea can represent either the transitions as mentioned above, or can be a physical representation of chaos. Titanic takes this to a whole new level, but even before the iceberg incident, in the movie we got to see the way certain characters were transitioning. And the chaos was forming on the boat before the iceberg as well.
There are revelations for characters in submarines too - like a favorite of mine (in spite of the fact that the Russian Captain has a Scottish accent) is The Hunt for Red October. 20,000 Leagues Under the Sea? U-571? There are all kinds of "water" movies where we see the transition a character experiences because of the waterly journey.
Either the river or the sea can also symbolize a passing of time. This is brilliantly done in Lisa Mangum's The Hourglass Door Trilogy. The river embodies the idea that people who go to it will never be the same and the passing of time.
Can you think of literature/movies when characters encounter water? What changes have you seen in them before and after their H20 experience?