There is an article based on research at Duke U and published in the Proceedings of the (US) National Academy of Sciences which links natural gas drilling in organic rich shale deposits and methane contaminated residential well water.
They found that the chemicals used for fracking didn't percolate but the methane they were extracting appeared to. The level of methane in wells was almost twice the permitted amount - not that there is any actual permitted amount, the federal regulation is a safety one, recommending that there be ventilation of the water containers!! Water containing methane is not harmful, but it can explode!!
They eliminated biological decay as a reason for the presence of the methane.
The article reports that the US Dept of Energy has set up a committee to report in 90 days on safety and environmental effects of fracking.
The industry associations have criticised the study saying there was no baseline of the amount of methane in the water before the drilling started.