The upholstery that covers a car's interior can uncover a flood cover-up, too, with close inspection. Take a careful look at all the upholstery — front, back and under the seats — to spot blotchy, brown water stains.
Another clue is the quality of the carpet. If the car is 10 years old but the carpet looks new, be suspicious. Likewise, if the upholstery doesn't appear to match, with sections that are a different color, faded, newer or with patterns that don't line up, then someone may have removed water-stained patches. Loose carpet, too, requires further scrutiny.
Don't forget to compare the floor carpet to the upholstery on the doors and the roof to be sure they all appear to be the same age and color.