It shall be unlawful to make any fill or deposit of rock, earth, sand, or other material, or any refuse matter of any kind or description, or build or commence the building of any wharf, pier, dolphin, boom, weir, breakwater, bulkhead, jetty, bridge, or other structure over, under, in, or within forty (40) feet of any navigable waters within the said Port District without first submitting the plans, profiles, and specifications therefor, and such other data and information as may be required, to the Port District and receiving a permit therefor; and any person, corporation, company, city or municipality or other agency, which shall do any of the things above prohibited, without securing a permit therefor as above provided, shall be guilty of a Class A misdemeanor. Any structure, fill or deposit erected or made in any of the public bodies of water within the Port District, in violation of the provisions of this section, is hereby declared to be purpresture and may be abated as such at the expense of the person, corporation, company, city, municipality or other agency responsible therefor, or if, in the discretion of said Port District it be decided that said structure, fill or deposit may remain, the Port District may fix such rule, regulation, requirement, restrictions, or rentals or require and compel such changes, modifications and repairs as shall be necessary to protect the interest of the Port District.