Fred,
The simple answer is that the quarry sits less than 50 feet for the stream. That section of stream has a fault on the bottom, the water flows from the stream into the quarry. There are pumps that are used to pump the water back into the creek. These pumps pump sometimes more then 30 million gallons of water out of the quarry every day.When the pumps don't work the stream suffers.
To me the only logical solution is to shut down the quarry. Once the quarry is full the water will return to the creek. It's a DEP issue, they permit the quarry, but they also regulate the quarry, a big conflict of interest.
They are NOT pumping out of the water table as far as I know. I believe they have emergency pumps, but they have failed more than once.