Lower courts MIGHT consider, but…...the Clean Water Act applies to all lands within the US including State land. Additionally, courts are unlikely to over rule a federal agency as long as all administrative steps were taken and nothing specifically contrary to law occurred.
The Dunleavy administration knows this and attempted to circumvent by filing with SCOTUS, but was rejected.
More importantly, the current mine plan is uneconomic. To move forward a new mine plan (underground only), 404 permit application and EIS is required.