The remnants of the Atlantean's magical ferry boat system still run throughout Oceanus, connecting each of the havens with each other. You can find the ferries at any of the docks near the havens. The name of the boat indicates which trial area it sails to.
To board a boat ferry, simply double-click on it and you will be automatically put on board. As the ferry approaches each dock, the passengers will be disembarked and placed on the shore. You can disembark from a ferry at any point during your voyage by hitting the 'jump' key (A by default).