Apparatus and methods for improved transportation functionality. In one aspect, the invention comprises an improved and highly integrated transportation apparatus adapted to bring a plurality of different modalities in close physical proximity for enhanced efficiency. One exemplary embodiment comprises a multi-level structure disposed in a substantially contained low depth body of water (e.g., bay) and proximate one or more land masses to facilitate service via rail, land vehicle, ships, and ferries. Multiple long-length runways are also provided on the substantially planar top surface to accommodate air traffic. A monorail or similar system is also employed to allow ready movement between the various transportation interfaces.