The interior of a flooded car will often smell musty or moldy due to prolonged exposure to water.  Always run the air conditioner system to see if it produces a moldy smell.

Moisture beads or fogging in the interior or exterior lights are a warning sign of possible flood damage.

Large stains on the carpet or upholstery of the vehicle could indicate water damage. Pull the seatbelt out completely to look for signs of moisture or mildew.

Engine smoke is a serious warning sign if you suspect the car has been flooded.

Look for rust on the underside of the car. A flooded vehicle will often have more rust than you'd expect for the car's age, as well as rust in odd places. 

Odd noises from the brakes or steering wheel may indicate that sand or dirt has gotten into these systems. Noises coming from a variety of areas may indicate flood damage.