Hello and thank you for using just answer. If water entered the engine this could mean BIG trouble. First I recommend you remove the air filter AND the spark plugs, crank the vehicle over a few times to remove any water that may have entered the engine. Let it sit for at least 24 hours to dry out and then reinstall the spark plugs and air filter (if the air filter was wet then you need to replace it. Also check the oil level, if it seems high then you need to drain the oil and replace it, water and oil don't mix.
Water in an engine can create a "hydro-lock" situation, basically what this means is that air can compress, water can't, if water enters an engine and it is forced to run until it stalls then it can cause internal engine damage such as bent valves or rods, once the car has dried out and you reinstall the parts then you will need to start the car, any unusual noises will indicate internal engine damage that will require costly repairs, you amy consider calling your insurance company at this point.