seven seas is manmade, the body of water that the monorail goes around and is in front of the magic kingdom. Bay lake is nature made and located behind the CR and that the wilderness lodge is on. They are connected with a water bridge.
If you've ever stayed in a Contemporary Resort tower room, you had a view of Seven Seas Lagoon if you had a Castle view. If you had a view of the pool, the boat dock and faced east, you were looking at Bay Lake.
Bay Lake is natural. After Disney bought the property, they drained the lake and found white sand. This is the sand they used for the beaches at the CR and Poly.