White foam in northeastern Pennsylvania water wells likely was caused by Marcellus Shale gas well sites that have already been blamed for causing natural gas to infiltrate residential water supplies, a paper published by the journal Proceedings of the National Academy of Sciences reported on Monday.

Environmental consultant Garth Llewellyn and biochemistry and geosciences researchers with Penn State University used a novel method to identify low levels of organic compounds that they said likely explain foaming from three water wells in Bradford County between 2010 and 2012. Test results from commercial laboratories during investigations at the sites had not picked up on what was causing the foaming — they reported no unsafe levels of compounds other than natural gas in the water, while other compounds, like glycols and surfactants, had appeared inconsistently or at barely detectable levels.

The same or similar organic compounds that the researchers traced in the water, including 2-n-Butoxyethanol, or 2-BE, are known to be used in drilling and hydraulic fracturing additives or to appear in waste fluids from oil and gas operations.

The researchers said it is impossible to “prove unambiguously” that the contaminants in the water came from shale gas-related activities because they were unable to secure samples of fluids that were used at or near the well site. But they said that multiple strands of evidence, including timing, well construction problems and the presence of matching compounds in both shale fluids and the water wells, make shale activity “the most probable source.”

The researchers do not suspect that fracking chemicals traveled upwards from the Marcellus Shale. Rather they said the most likely explanation is that the compounds were driven about 1 to 3 kilometers along natural underground fractures to the aquifer. The trigger might have been drilling, fracking or the leaking pit, the researchers said, but a particular point of weakness identified was an uncased section of the well deeper than 300 meters underground that intersected with an existing fault.

Pennsylvania regulators have since strengthened drilling rules to require additional strings of cemented steel casing in shale gas well bores to keep gas and fluids from escaping.

Chesapeake Energy, the company that drilled the suspected wells, was fined $900,000 in 2011 for allowing natural gas to contaminate water supplies in Bradford County. The Oklahoma City-based company reached a $1.6 million settlement with the homeowners in 2012. The company declined to comment.

A spokesman for the Marcellus Shale Coalition, a North Fayette-based trade group, said that significant technological advancements and stronger regulations have been developed in recent years to protect groundwater, “which is a top industry priority.”

Mr. Llewellyn, the paper’s lead author, and his firm Appalachia Hydrogeologic and Environmental Consulting, provided litigation support and environmental consulting services to the impacted households, the paper disclosed.

Mr. Llewellyn said that the state’s investigation and the private case focused on natural gas contamination, but he remained puzzled by the foam, which he likened to dishwashing suds.

Penn State researchers used a tool called 2D gas chromatography coupled to time-of-flight mass spectrometry, which allowed them to identify classes of contaminants, like hydrocarbons, without pinpointing individual chemicals one by one.

The researchers said their results raise questions about the sufficiency of conventional analytical techniques to explain water impacts in some cases.

Normally, very low detections of compounds could be dismissed, but the persistent foam indicated something was wrong, Penn State geosciences professor Susan Brantley said.

The study is not the only time shale gas activity has been implicated in causing thick suds in drinking water or groundwater in the state.

Last May, the Department of Environmental Protection found 2-BE and other chemicals in a Susquehanna County water well after a resident complained of rank, foamy water. DEP said the chemicals were consistent with the surfactant Air Foam that was used to drill a natural gas well 1,500 feet away.

In 2011, DEP fined Pennsylvania General Energy Co. $28,960 for discharging Airfoam HD from a Marcellus Shale well bore to a spring and into Pine Creek in Lycoming County.