A system for the transfer, storage and distribution of intermodal containers of a plurality of lengths. The system comprises a first storage area comprising a first plurality of shafts arranged in a grid pattern along a first and second axis, a plurality of gantry cranes slidably disposed along the first axis and extending beyond the storage area, a roof structure disposed at a distance above the plurality of shafts, and a plurality of overhead cranes slidably associated with the plurality of tracks. The shafts disposed in rows along the first axis are configured to store intermodal containers of a plurality of lengths. The shafts disposed in a given row along the second axis are configured to store intermodal containers of a corresponding length. The plurality of gantry cranes are each configured to attach to and transport an intermodal container from a first location to one of a plurality of platforms slidably disposed along the first axis. The platforms delivering the intermodal container to one of the rows of the shafts along the first axis are based on the length of the intermodal container. The roof structure comprises a plurality of tracks corresponding to the rows of the shafts along the second axis. The overhead cranes are each configured to attach to and transport the intermodal container from the platforms to either one of the shafts or to a second location.