During the year of Hurrican Katrina, hurricanes in the Gulf Coast have left thousands of homes, factories, schools and vehicles under water. Structures can be rebuilt and streets can be repaired, but is there any way that these waterlogged vehicles can be brought back to serviceable life? Yes there is, but resurrecting a car that's been in a flood is going to require time-consuming work and attention to detail. It's not quite as dramatic as a frame-off restoration, but it will take a lot of work.
Things wouldn't be as bad if the flood water wasn't so filthy. If your car fell into a swimming pool and you got it out and drained the water, chances are the overall amount of work (relatively speaking) to get the car back on the road wouldn't be all that great. Swimming pool water is clean and mixed with chlorine, so many of the effects seen from flood waters wouldn't be of too much concern. Chief among these effects is mold.
This disgusting stuff consists essentially of fungus micro-organisms whose spores thrive in a moist, warm environment to become what we know as "molds." They derive their food from the substance on which they form. During their growth they produce citric, gluconic, oxalic, or other organic acids that can damage paper, leather, cloth, etc. They also at times produce color bodies that lead to staining. Of greater concern is their ability to create toxins that are potentially harmful to humans. They are, in short, very bad things to have around.
Carpet, upholstery, foam rubber and insulation in a car are great places for molds to form and grow, which is why so many older cars have moldy interiors in spite of never having been in a flood. Imagine, therefore, how easy it would be for molds to grow in a car that's been underwater! The lesson here is that, at the very least, your flood-damaged car's interior is going to have to be removed. Whether any part of the interior trim is salvageable or not is another question, but prudence would dictate replacing everything unless a cleaning/disinfecting could be accomplished on the original materials.
The dash is no exception, by the way. Your dash covering materials will have to be stripped off and all instruments must be taken apart and cleaned with appropriate solutions. Electrical contacts must be cleaned and treated with anti-corrosion compounds if there is a buildup of crud on them. Speedometer and tach cables should be removed and drained of water, after which they need to be lubricated.
Wiring harnesses are waterproof, so all that needs to be done is to clean them thoroughly. This can be done in place, however, because you've already stripped out the interior. A mild detergent/disinfectant solution spread with a pressure washer (on a gentle setting) is a very effective way to clean harnesses. The pressure washer can be used to clean all the interior surfaces as well. After cleaning, spray the whole surface area with Clorox (or any other brand) and wipe it dry. It will kill any leftover organisms.
Wiring connectors are not waterproof. You'll need to disconnect every one and clean it thoroughly, preferably with spray contact cleaner (trichloroethylene). Seat channels and window regulators need to be cleaned and lubricated.
If the car was completely underwater you can be sure that the engine is filled. You probably don't have to take it apart, however. Pull the dipstick and look for water/mud to verify, after which you should drain the oil and remove the pan. Any mud left over can be cleaned out. Remove the exhaust system entirely and stand up all the components so that they can drain and dry out. If there's mud in them you'll have to pressure-wash them out, but otherwise they'll clean up inside once the engine is running again.
Look into the exhaust ports. If there's only water in some of the cylinders you can suck it out with a shop-vac. Don't forget to remove the intake to get at any water on the top side of the cylinders. If there's mud inside the engine your best bet is to take the heads off and clean out the cylinders. Spray the cylinders with fogging oil.
The cooling system is sealed, so there's no need to worry about the radiator's internals. However, mud and other nasty stuff is likely to be clogging the fins so crank up the pressure washer and clean it - and the A/C condenser - thoroughly. Clean the entire engine bay area as well, paying particular attention to the wiring harness and suspension points. All connections are going to have to be pulled apart and cleaned as above.
Once it's all cleaned check the power steering pump reservoir and brake master cylinder. If there's any trace of contamination, suck out the fluids with a siphon to determine how much waterborne material got in. Replace the window washer fluid and clean the lines.
Your alternator or generator was immersed during the flood, so it's likely to be ruined. You can pressure wash it out but be prepared to replace it. The same goes for the starter motor and the clutch pressure plate, but for the moment you might as well leave them in place.
The brake system components need to be cleaned as well. Drum brakes should be disassembled to get at the inside pieces. There's no need to remove lines if the hydraulic system is intact.
Transmissions and differentials have vents. Water might have seeped into them from these vents, so you need to drain all the gear oils and look for contamination. If things look good, refill and hope for the best. If muddy water comes out you will have to consider taking the assemblies out and opening them up. Automatic transmissions are more likely to remain sealed, but water might have seeped into the dipstick tube. If so, you'll need to drain the transmission by removing the pan.
Water also will have seeped into suspension grease points, so clean the outside of each fitting and pump new grease in. This will push any water and dirt out.
Don't forget the car's frame. It's usually hollow, with a number of holes punched in it for tubing and wiring access and for drainage. It's probably full of mud or water, so get the car up on jack stands and pump fresh water into any accessible holes with the pressure washer. Keep doing so until only clean water comes out.
Now we come to the fuel tank. If the filler or vent weren't under water you are essentially home free. If, however, the whole car was immersed you'll have to drain and remove the tank and then clean it out. If it's more than 30 years old you're better off replacing it, but it's your choice.
As for the body exterior, there's mostly good news. Paint is pretty resistant to the effects of water, even muddy water. You should be able to wash it off and wax out any minor scratches and abrasions. Don't forget to pressure wash inside the fenders.
Once all the cleanup and mold prevention is done you can get the engine started. Make sure fresh gas is getting to the carburetor/fuel injection and there's clean oil in the crankcase. It's better to get the engine going initially without the exhaust manifolds, to facilitate blowing out residual crud. Also, if the engine's bearings fail it's much less work to get it out for rebuilding.
Assuming the engine runs okay, test the clutch (or automatic gear selection) for smooth, noise-free operation. If that works correctly it's safe to reassemble the exhaust and take the car for a test drive. Only after that is it reasonable to reinstall the interior trim.
As anyone can see, getting cars operational after flood damage isn't trivial. That's why insurance companies usually "total" such cars rather than pay to have them rebuilt. The same goes for new vehicles, so be wary of great-sounding deals these days. They might be too good to be true!