For the improvement of water quality in a harbor, several studies have been carried out on SEB (Seawater Exchange Breakwater) in recent years, but a problem has been shown whereby the water on the inside area far from the SEB cannot be easily exchanged. In order to solve the problem of the SEB, the Manifold channel, a new concept of the SEB, is introduced in this paper. By using the manifold channel, it is possible to exchange the water of the inside area for seawater from the outside. Here, to assess the outflow gates of the manifold channel governing flow behavior, a virtual manifold channel controlled the location, width and direction of outflow gates applied to the Jumunjin fishery port, where the SEB has been established. In addition, the desirable flow pattern of the port by utilizing the two layer current model is identified, and five general cases of the manifold channel are described in this paper. The model is verified by comparing with observation of the SEB model, and the results are in general agreement. From the results of the manifold channel, in the case of the Jumunjin fishery port, the small circulation of counter clockwise is necessary for the water exchange on the inside area, but it should be controlled by the outflow gates for other areas. Using the two layer current model, the desirable flow pattern of the port can be predicted, and the water exchange for the upper and lower layer can be examined. For the practical use of the manifold channel, further studies on the manifold channel will be necessary, and it may then be used broadly for the design of breakwater in the future.