Ask oil and gas industry advocates, environmentalists and regulators about the biggest issues facing shale gas development, and none are likely to cite the possibility of fracking fluids traveling up thousands of feet of rock into groundwater aquifers as their top concern.

There’s surface spills, transportation accidents, leaks in holding tanks and impoundments — all of these have much more potential to pollute groundwater.

Yet blaming — or exonerating — fracking for this method of groundwater pollution seems to lead reports of new shale studies, even if those studies say little about actual fracking.

“Faulty well integrity, not hydraulic fracturing deep underground, is the primary cause of drinking water contamination from shale gas extraction in parts of Pennsylvania and Texas, according to a new study by researchers from five universities,” began a press release last week from Duke University, former home of Rob Jackson, one of the scientists involved in the study.

The study, one of several for Mr. Jackson dealing with groundwater contamination from shale development, used noble gases and more traditional gas fingerprinting techniques to trace the origin and pathways of methane traveling into groundwater.

It suggested that leaks in either the steel pipes that carry gas to the surface or in the cement that envelopes those pipes allowed methane to escape into shallower depths, causing changes to well water supplies in Pennsylvania and Texas.

The study did not examine whether the pressure exerted on the well’s layers during hydraulic fracturing contributed to or caused the casing to become compromised.

Fracking is a confusing and often misused term that refers to the process of shooting millions of gallons of liquid and sand through holes in a wellbore to break open the earth where oil and gas is trapped.

Many in the oil and gas industry are irked when people use “fracking” synonymously with “shale gas extraction,” noting, correctly, that it’s only part of the process.

But laypeople get annoyed when they are told fracking has never been proven to contaminate anything, arguing hydraulic fracturing doesn't occur in a vacuum but is inextricably linked to every other part of the gas extraction process.

Mr. Jackson can see both sides.

“For professionals, the difference between fracking or well integrity causing contamination matters. It points to a different set of solutions,” said the researcher, now at Stanford, whose new study was at once heralded as further proof of fracking’s benevolence by the industry-run website Energy-in-Depth and refuted for other reasons.

“For people whose water has been contaminated, though, they don't care what step caused it. All they know is that they're afraid to use their water,” he said.

And those in the business shouldn't just shrug that off because affected citizens use imprecise language, he said.

“I think industry has a tin ear sometimes with ‘fracking never causes contamination.’ The entire process is enabled by fracking and horizontal drilling. Peoples’ water has been contaminated. They should acknowledge it and work to keep it from happening elsewhere,” Mr. Jackson said.

Still, definitions aside, the issue of whether induced fractures in a well could stretch far enough to carry fluids to the surface or to underground aquifers isn't a pressing scientific question.

“Decades of work have revealed that” it isn't likely, said Fred Baldassare, who spent 25 years as a methane expert with the Pennsylvania Department of Environmental Protection before founding his own consultancy, Echelon Applied Geoscience Consulting in Murrysville. He now works with oil and gas companies to identify cases of methane contamination from extraction activities.

As has been the case for most of his career, Mr. Baldassare is primarily concerned about methane migration, which could happen if the gas moves up through cracks in the well casing or if shallower gas is disturbed and displaced by extraction activities.

While methane itself isn't toxic, it can change water chemistry and deteriorate water quality by stirring up different compounds and causing chemical reactions that introduce a foul smell or black coloring into water.

“The methane issue is really the 800-pound gorilla,” he said. “But there’s a whole host of issues.”

The focus on fracking can distract from other, perhaps more relevant, concerns with shale gas extraction, such as waste disposal, surface spills, radioactivity and emissions, experts say.

“For me, as a resident in the Commonwealth, my big concern is truck traffic,” Mr. Baldassare said. “I look at risk and I see these roads were not built for this.”

At the Environmental Defense Fund, a New York-based advocacy and research group, water contamination through fractures isn't mentioned in any of its numerous concerns with gas extraction. EDF is one of a handful of environmental organizations that has partnered with the oil and gas industry on best practices and regulatory standards.

“It’s sort of been a source of frustration for the folks here,” said Lauren Whittenberg, a spokeswoman for EDF. “Gosh, it always comes back to fracking, but it’s so much more than that.”

Air emissions take top rank among EDF’s concerns for shale gas extraction, said Scott Anderson, senior policy director of the organization’s climate and energy program.

Then there are well integrity issues, waste management, community impacts and enforcement to be concerned with.

“The environmental footprint of the industry goes far beyond the question of whether, how and how often frack chemicals get loose,” he said.