The moment you have your line fully wheeled down, you have a 1000 ft line with a 1 kg weight on it. Even at your 400 ft (well over 100 meters) limit that's indeed bound to start swinging around, and your drone may not be able to compensate for that. That's one massive pendulum and there's always wind, if only from the drone's rotors, to start a swinging movement.
As you mention it's to be lowered under water - so you can mitigate this problem by having it winched all the way up when starting off, then lowering your drone as low as possible above the water and start unwinding. The water should stop it from swinging - but you will have a serious problem if there's any current in the water you lower your load in, as the pull of the current will easily overpower your drone.