Flying over water is just like flying over land. The major difference is that your Phantom will most likely be unrecoverable if it auto lands in the water for some reason. Make sure you start with a full battery and be mindful of the battery voltage to ensure you can return it back to the home point safely.
It's most important to make sure your Phantom does not touch the surface of the water. If you must fly very close to the surface for some reason, then make sure you can easily see your Phantom with your eyes. Otherwise, you'll be just fine in most cases even when VPS is enabled. If your Phantom is at an altitude where VPS is able to detect the ground (between 0.3 to 10 meters) and it starts drifting, either ascend or disable VPS.