Just like wrecked vehicles. I have seen cars with clean titles that I wouldn't rebuild if they gave them to me and bought the parts. Conversely I have seen cars with salvage titles that you could drive home. It just depends on what happened to them.
One of the quickest giveaways for a water car is the smell when you open the door. If it smells musty or the humidity level seems usually high, it is a possible water car. You can also check the oil, transmission, power steering and other fluids to check for a milky color. If the fluids have a milky color, the water got at least deep enough to contaminate that part of the vehicle.
A couple other areas that are overlooked are the lights. Excess water in the headlights, parking lights or taillights will remain in them longer than you would think. If you see water beads inside the fixtures, you need to ask questions. And check the instrument panel to see if there is some unexplainable "dirt/dust" inside the gauges. With some vehicles, it is hard to get these perfectly clean.
A couple other places you can check if you have the time and are allowed to are the upholstery and inside the trunk. If you see water marks either place, ask questions. Check inside the trunk in the corners for silt residue, especially behind the wheel wells in any low areas. If you are allowed to, it would not be too much to at least pull a door panel and check the inside of the bottom of the doors. A couple of things that people should know about water cars though. They can be returned to as good as before the submerging, but it generally requires a lot of effort and is an ongoing adventure. First of all you need to determine the type of water the vehicle was in, then to what depth it was covered up, how long it was under and what was done to it immediately after the waters receded.
Salt water obviously is a lot more potentially damaging to the vehicle over a longer period of time. DIRTY fresh water is the next type down the totem pole as dirt and silt and the like will find places that you couldn't imagine existed when you looked at the car. These two require a lot more work to fix than the last type (generally speaking) of FRESH water immersion. This still has some dirt, etc in it, but is a lot easier to clean up.
When cleaning up the water car, you will need an ample supply of of dry rags, compressed air, heavy duty vacuum cleaner, and WD40 as well as a lot of time, patience and room to spread out things that you remove form the car. After you have done the best you can to clean up everything externally, the mechanical side has to be addressed. And what you have to do here depends on how deep and how long the vehicle was in the water. The more time in deep, the more work to do.
Could be anything from cleaning the motor, trans, rear end, etc and changing filters to tearing EVERY component down and cleaning every little piece. If the water (particularly the first two) gets over the breather, you are looking most likely at a major engine teardown, if not then almost for sure eventually. It will amaze you how much sand and silt can get into places it isn't supposed to. If the trans and rear are sealed units this may or may not be necessary, but you need to keep it in mind when looking at a suspect vehicle. One other thing to remember about water cars. You can take as much apart as reasonably feasible, shoot WD40 (or similar rust inhibitor) on the exposed metal pieces (i.e., power window motors, door mechanisms, etc) and clean until you think everything is perfect, and if you keep the vehicle a lot of the electrical/mechanical pieces will still need to replaced or recleaned over a period of time. I don't say this to scare people off from these cars, but only for your edification. Flood cars can be repaired to as before, but in some cases it takes more effort than others....
Funny part about it is, that I was thinking about the same thing today. Bet the yards in Virginia, NC, and the rest are going to be loaded for a while until they can cycle these vehicles out again..... And they will have every thing imaginable in their yards to sale......
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