I all depends on how bad and how long! First thing is to drain out all the oils and replace them, also the gas tank needs to be drained and the lines "blown out" with compressed air! You want to make sure all the electronic components (especially the computer - if it has one) are fully dried out before applying power to ignition circuit! The interior has to be dried out, and of course at some time cleaned up! All the above information refers to a car that has been under water!
If the water didn't totally submerge, the car, anything above the water line shouldn't give you a lot of trouble, and if the amount of time was submerged for "hours" rather than days, the project becomes easier also!. I have "gone over" several cars that have taken a "dunk" in the river or lake! They were pulled out within 2or 3 hours! They weren't real problems, except for water damage to interior,and "water soluble" products!
If I were starting on a car for myself here is the sequence I would go through! First make sure the computer "area" is dry and "free of debris", -- if it is still wet in that area, unplug and remove the computer(s) and put them in a "clean area to dry"! Electronic circuit boards don't like water or moisture!
Next remove the sparkplugs, and put on a battery with a good charge, - see if the engine will turn over with starter! If the engine spins over ok, you are ready to "go" for putting it back on road.
If the engine is "locked up" and won't spin over, you might want to stop there, and find out if the engine is any good! If not,- there is no point on going any further, (and wasting more money) !
Now you can dump the engine oil and change the filter, - and refill with oil, - it should be ready to go! (Sparkplugs still out).
next drop the oilpan on transmission (or pull drainplug on standard), - drain oil, (replace trans filter on auto, - it's good time, as pan has to be pulled to change filter). At this point the "drivetrain is pretty well covered (if it is a front wheel drive), - If rear wheel drive, - you should drop and change oil in the rear axle (reared) also! At this point, - I would crank engine over about 2 minutes, at about 30 seconds to a "burst" with 30 second wait between cranking "bursts", - this will clear all the water out of the induction system of engine. You can now put the sparkplugs back in!
Part 2: Determine if filler neck of gas tank was below water level! Also whether it was full of gas at the time or near empty, a "full tank" will let in very little water , - (unless it is submerged for quite a while!) If it wasn't under water, you might just try going to the drugstore and getting 2 or 3 pints of isopropyl alcohol (rubbing alcohol), --This will absorb about equal amount of water, - and pull it through the induction system, and burn it along with the gas! If it wasn't under water, it actually should have no water in it, but it is a good "insurance system"!
Don't forget the brake fluid, - if the car has been under deep enough to submerge these", -- if it has been submerged, I would take it to a garage, and have them "backflush" the brake lines and master cylinder to make sure all the water is removed (as water is real hard on brake components when it gets in lines and cylinders!) You should be able to do this after you can "drive" it to garage! ... Also you might want to get the power steering fluid "flushed out at a that time also, (if it has gotten water in it).