S.C. Code § 49-1-16
The Department of Health and Environmental Control may charge a fee to an applicant for a permit for any construction, alteration, dredging, filling, or other activity in navigable waters of the State. If the project is commercial or industrial and is in support of operations that charge for the production, distribution, or sale of goods or services, a fee of five hundred dollars must be charged, except if the aerial crossing of navigable waters by conductors or other wires supported solely by structures outside the navigable waters the fee shall be one hundred dollars. If the work is noncommercial in nature and provides personal benefits that have no connection with a commercial enterprise the fee must be fifty dollars. The department shall remit the fees to the State Treasurer and shall be issued a credit for any portion of the fees necessary to offset its costs in processing, investigating and taking final action on each permit application. Any remaining portion shall be credited to the general fund of the State.
S.C. Code § 49-1-16
2010 Act No. 247, Section 4.B, provides:
"Chapter 1, Title 49 of the 1976 Code is not affected by and supersedes Chapter 4, Title 49 of the 1976 Code, as amended by SECTION 1 of this act."