The biggest threat by far is the management of the resource, and IMO there isn't a close second.
Run off is essentially a non issue because the 3 tribs are in decent shape, especially Cane and Clear creeks. Coal creek probably puts a little nastiness in the river but it is very minor.
Stripers pose a small but easily fixable problem.
In general water quality is excellent and we are fortunate in that regard.
One thing to note; New river, and any of the other streams that form in Scott county or the plateau where various forms of mining occur have zero impact on the Clinch. Those are entirely different watersheds and could not pose any threats to the Clinch. Currently there is no active mining in the Clinch watershed and the old mines have far surpassed an age of causing any issues.