You have to drain the tank.... you have to eliminate this variable first.
Stop driving your vehicle if you still have water in fuel...... you will do major damage to the high pressure fuel pump and or injectors.
1. Remove the fuel line leading into the fuel filter from the fuel tank and use it to drain out the bad fuel in the tank. Use 5 gallon buckets to hold the bad fuel, use piece of an old garden hose as a funnel to drain the fuel into the buckets.
2. Turn the ignition key to on but do not crank the motor so that the lift pump can do its work in removing the fuel from the tank.
3. Allow all of the fuel to drain out of the tank, it will take some time.
4. Add 3/4 can of this stuff
http://www.powerservice.com/d911/ to the fuel tank.
5. Unscrew the fuel filter and drain the bad fuel out of it then add 1/4 can of this stuff
http://www.powerservice.com/d911/ and good fuel to the fuel filter then screw it back on.
6. Add good fuel to the tank.
7. Start your vehicle.
8. The water issue should be gone, if not then you have other issues.
9. If your dealer is of little help, then locate a reputable local diesel mechanic for assistance and advice.