As you can see in the One Piece manga Chapter 1089, there is a giant hole in the ocean. It was the result of a mass destruction weapon tested six days ago by the orders of Imu-sama to destroy the kingdom of Lulusia. The attack resulted in the formation of a giant hole shaped like a circular waterfall in the middle of the sea.
The World Government dispatches its agents to investigate the location to ensure no traces of Lulusia remain. The attack also triggered massive earthquakes, raising the sea level worldwide by about 1 meter.
Could this explain the origin of the massive waterfall in Enies Lobby?
Source: https://kaptentekno.com/one-piece-1089-the-giant-hole-resembling-enies-lobby