It is 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, or near any navigable waters within the Port District without first submitting the plans, profiles, and specifications, and any other data and information as may be required, to the participating municipality in which the project is located and receiving a permit. A person, corporation, company, municipality, or other agency that does any of the things prohibited in this Section without securing a permit as required in this Section shall be guilty of a Class A misdemeanor. However, a permit is not required (i) for any project for which a permit has already been secured from a proper governmental agency prior to the creation of the Port District or (ii) for a project to be undertaken by a participating municipality for which a permit is required from a governmental agency other than the participating municipality before the municipality can proceed with the project. 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 a purpresture and may be abated at the expense of the person, corporation, company, municipality, or other agency responsible for the violation, or, if, in the discretion of the participating municipality where the project is located, it is decided that the structure, fill, or deposit may remain, the participating municipality where the project is located may fix a requirement, restriction, or rental or require and compel necessary changes, modifications, and repairs to protect the municipality’s interest.