Again, this has to do with the existing CWA, the separation of powers, and the implementation of existing sections of the CWA. See Old Paratrooper's comment above. It summarizes it nicely.  The CWA is still in effect, polluters are still being fined, and the water quality in the United States continues to improve (even before this rule was thought of).  

Obama's Executive Order that formed the Office of Surface Mining's Stream Protection Rule was a one-size-fits-all hammer to cripple the coal industry.  It did not take into effect different regional or local environmental conditions, geology, weather, runoff, etc.  

The laws that govern runoff and "scrape-offs" and the resulting water quality under the CWA from coal mines are still in effect and protective of the environment.