A study conducted by researchers at Duke University and California State Polytechnic University found natural processes were leading to some levels of contamination in drinking water wells and aquifers in northeastern Pennsylvania.
Pennsylvania hosts a portion of the Marcellus shale play, one of the largest sources of natural gas in the United States.
Shale natural gas extraction is controversial. There are concerns that some of the waste associated with the extraction methods could find their way into drinking water supplies.
Scientists found that salty water laced with certain chemicals like barium or compounds like methane were from natural pathways of contamination.
Robert Jackson, an ecologist at Duke University and one of the report's authors, said the mineral-rich fluids are seeping upwards through the shale layer.
He told National Public Radio scientists were working to figure out what was coming from shale gas extraction and what was from natural processes.
"They are a possible conduit for movement of salts or fracking chemicals or even gases up to the surface," he said. "But we just don't know how likely that is."
The study was published in the journal Proceedings of the National Academy of Sciences.