Development of unconventional energy resources if often associated with public concerns regarding potential contamination of shallow groundwater due to methane leakage. We combined chemical and isotopic analyses of gas and water samples obtained from shallow aquifers in Alberta (Canada) to assess baseline methane sources and found that > 67 % of the samples contained biogenic methane formed in situ in the aquifers. There was no evidence of deep thermogenic methane migration into shallow aquifers.