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The authors developed a wave dissipating caisson breakwater having a function of seawater exchange. This caisson is a permeable slit caisson with a submerged vertical plate in a water chamber. This caisson generates a one-way flow from offshore to harbour. This flow enhances the exchange between contaminated harbour water and clean offshore water. Originally, this caisson was intended for calm sea. However, the function of seawater exchange came to be required even for outer breakwaters at large harbours facing rough sea. In offshore areas the width of a caisson must be extended to resist against strong wave forces. Therefore, the caisson needs to have channels piercing itself. In order to make clear its hydraulic characteristic, a two-dimensional hydraulic model experiment was carried out. It revealed that the channels never spoiled the seawater exchange, even in the condition of smaller wave height.