Coal had been mined commercially for nearly 75 years before there were any studies about why water quality in the Stonycreek River and its tributaries was so impaired. The first study, in 1970, documented the culprit—abandoned mine drainage—and at least nine subsequent investigations over nearly three decades merely refined the argument while expanding the number of known discharges and AML sites. Probably the US Geological Survey's (USGS) three year study, released in 1996 and by far the most comprehensive to that point, was the "game changer." It identified 270 AMD discharges in the watershed, 85 percent of which tested below Environmental Protection Agency water quality standards on one or more criteria, for pH, total iron, and total manganese. (40 of the 270 sites failed on all three counts.)
Between 1993 and 2012, through the public-private partnerships created by and coordinated through the Stonycreek-Conemaugh River Improvement Project (SCRIP), the watershed became home to nineteen passive treatment systems and two AML reclamation projects. In assessing the importance of such projects, the Somerset Conservation District's 2008 Watershed Reassessment concluded that in the intervening period (more than a decade), the Stonycreek River had changed "from a net acidic to a net alkaline stream, as a result of increased alkaline inputs from passive treatment systems." This was a good start, but not enough.
In its evaluation of the physical habitat, water chemistry, macroinvertebrates and fish populations at 35 sites along the Stonycreek River and its tributaries, the Watershed Reassessment also concluded that 18—half of the total evaluated—were "severely degraded by some combination of acidification, organic loading and physical habitat degradation." Seventeen were classified as "moderately impacted," and only four sites were judged pristine, "excellent quality streams." Agriculture and coal mining were identified as the leading causes of stream impairment.
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