Applicants whose activities are certified or conditionally certified by the executive director, or for whose activities the executive director waives certification or takes no certification action based upon the applicant's agreement to include permit terms or conditions in the federal permit, shall comply with all terms and conditions of the permit as issued by the federal agency and as thereafter amended. Violation of the agreement to include permit terms or conditions, or violation of any term or condition of a permit relating to water quality shall constitute a violation of this rule. The commission may enforce such a violation under TWC, Chapter 7, and Chapter 70 of this title (relating to Enforcement).