To issue permits for the construction of all wharves, piers, dolphins, booms, weirs, breakwaters, bulkheads, jetties, bridges or other structures of any kind, over, under, in, or within 40 feet of any navigable waters within the Port District; for the deposit of rock, earth, sand or other material, or any matter of any kind or description in said waters; except that nothing contained in this Section 5.2 shall be construed so that it will be deemed necessary to obtain a permit from the District for the erection, operation or maintenance of any bridge crossing a waterway which serves as a boundary between the State of Illinois and any other State, when said erection, operation or maintenance is performed by any city within the District.