The grand jury report said the company hauled sludge from sewage treatment plants, grease water from restaurants and fast-food chains that can't be sent to normal sewage systems and the wastewater produced by wells drilled into the Marcellus Shale natural gas formation.
The southwestern corner of Pennsylvania is among the most intensely drilled regions in the Marcellus gas drilling rush.
Investigators accused Shipman's company of illegally dumping waste at several locations, including a brine disposal well called Morris Run, which had come under scrutiny for lax security and possible environmental problems.
In 2009, the EPA fined the well's owner, Consol Energy, of Canonsburg, Pa., $158,000 for failing to keep gates locked or properly log the trucks coming and going from the site. Federal inspectors also raised concerns about the contents of the waste being dumped, saying they suspected sewage was illegally being added to the mix of fluids.
State regulators asked the EPA to shut down the well in 2009 after a nearby waterway, Dunkard Creek, turned salty, feeding an algae bloom that choked off life and killed fish in a 30-mile stretch. Its cause has not been conclusively identified.
Shipman also has been accused of dumping into a waterway that feeds Dunkard Creek.
Ken Dufalla, president of the Izaak Walton League of America chapter in Greene County, said deteriorating water quality in Dunkard Creek and other tributaries of the Monongahela River in that area have led many local anglers to conclude there must be illegal dumping going on.
"If there's a businessman dumping in his back yard, if it's true, it is utterly outrageous, because we all live here," said Dufalla, whose conservation group has grown from 19 members to 101 in the past year, largely driven by concerns over the Marcellus shale drilling.
"If he is proven guilty, then shame on him. If he is not guilty, then good for him. But it is disappointing that a local individual, if involved in this, would do such a thing, because he's our neighbor. And it hurts, to be honest with you."
The company's lawyer, Christopher M. Capozzi, said he was still reviewing the grand jury report that was issued with the charges but noted they did not make specific claims of environmental damage.
"I didn't see any allegations to that effect," Capozzi said. "So it seems to me, if that was a concern, the attorney general's office would have mentioned it."
Prosecutors said that Shipman routinely told his drivers to combine waste material into a "cocktail" to help conceal its ingredients and to falsely inflate the volume of hauled material for billing purposes.
The presentment said a municipal sewage authority, concerned that Allan's Waste Water Service was illegally dumping sludge in Greene County, alerted the state Department of Environmental Protection, and the agency contacted the attorney general's office.
Katy Gresh, a Pittsburgh-based DEP spokeswoman, said the agency was reviewing the permits issued to Allan's Waste Water Service to handle such material. She declined to comment on the potential environmental impact of the illegal dumping authorities say occurred.
Court records say the company is located in Holbrook, about 60 miles south of Pittsburgh; Shipman's addresses were listed as Holbrook and New Freeport.