It is necessary to understand the presence, movement, and persistence of contaminants in aquifers to develop adequate groundwater protection plans. Fractured bedrock aquifers with thin overburden cover are very sensitive to contamination, and little is known about transport processes from the ground surface to depth in this setting. This study was undertaken to investigate the potential of groundwater contamination by polybrominated diphenyl ethers (PBDEs), which are flame retardants, in a natural fractured bedrock aquifer in Canada proven to be sensitive to contamination. PBDEs, which had not been previously measured in groundwater in detail, were detected in the study aquifer at concentrations greater than those observed in surface-water bodies. Potential sources include manure, septic tanks, and the atmosphere. From this scoping study, it is evident that additional surveys of PBDE concentrations in groundwater are warranted, especially in settings with high potential source concentrations coupled with sensitive aquifers.