Here's a recent article on Pebble Mine and EPA.
To fully understand the story, you need to know that EPA has authority under 404(C) of the Clean Water Act to veto Federal decisions that have a signficant adverse impact on water quality. However, they rarely use this authority. It's only used in the most extreme cases. Their veto authority has always been used to veto a decision AFTER a decision has been made. For example, if the U.S. Army Corps of Engineers issues a dredge/fill permit to destroy a wetland, EPA can veto the project based on 404(c).
Perhaps the most visible use of the 404(C) authority was in 1992 when EPA vetoed the Two Forks Dam proposal just outside Denver. It was a huge irrigation dam that would supply Denver with water for their lawns. That veto was upheld all the way to the White House (the first GWB). In the Great Land, just last year EPA was asked, but refused, to use it's 404(C) authority to veto a new bridge over the Tanana River just outside Fairbanks.
The issue here is that EPA is considering using it's authority BEFORE any decision is made on Pebble Mine. Vetoing a decisions before it's been made would be new. Really new. Some folks don't believe EPA has that authority. I'm not sure they do either. But if you read the very last line of the above story, you can understand why some folks are nervous.......