If you have had water damage to your vehicle you would need to make a claim with your insurance company through your comprehensive coverage. This type of physical damage policy covers things "other than collision" such as damage to your car if it is stolen or damage caused by flood, fire, or animals.
An insurance adjuster will then be assigned to the case and view the vehicle to see what the damage is and to determine if the car is repairable or if it is what is termed a "total loss."
Totaling out a car typically means that to repair the vehicle to the condition it was before the damage occurred would cost near or more than what the car is actually worth. In cases where the damage is that severe, the car is totaled out and usually the insurance company would settle with the owner for the actual cash value (ACV) of the vehicle.