I don't think I'd take a chance if the water it has been was very deep. I'd drop the pan and see what the ATF looks like. If it looks like a strawberry milkshake, it may be too late since water disolves the glue that holds the clutch disks in place. At that point, the best thing you can try is to have a complete ATF flush & replace.
If the ATF doesn't look like a strawberry milkshake, make sure the ATF level is correct and the fluid isn't burned. The correct way to check the ATF level is to get the engine up to normal operating temperature, shift though all the gears, then leave it in Neutral with the engine running and the parking brake set while you check the ATF level.