Miss. Code § 49-27-23
The commission may grant, issue, reissue, modify, deny, suspend or revoke permits and may prescribe limitations and conditions on permits. When taking such action on any permit, the commission shall consider the effect of the proposed activity with reference to the public policy expressed in Section 49-27-3 of this chapter. A permittee under this chapter must obtain a permit from the Mississippi Commission on Environmental Quality if required by that commission under Sections 49-17-29 through 49-17-43, and nothing in this chapter is intended to waive the requirements and standards of such commission. A Mississippi Commission on Environmental Quality permit granted to an applicant under this chapter shall be proof of the applicant's meeting any water quality standard considered by the commission under this chapter. Any conflict under this chapter between the commission and the Commission on Environmental Quality shall be resolved in favor of the Commission on Environmental Quality. The commission may undertake studies regarding water quality and submit the results of such studies to the Commission on Environmental Quality.
Miss. Code § 49-27-23