Gas migration incidents, particularly stream contamination cases, have been rarely investigated and gone through the peer review process, with the exception of three sites in northeast Pennsylvania (Dimock and two Sugar Runs in Lycoming and Bradford counties, respectively) where air emission surveys, dissolved methane measurements, and structural (hydro)geologic interpretations have been used to demonstrate potential environmental impacts due to shale gas operations. In addition to reviewing previously published work from these three sites, we report and analyze unpublished new data trying to determine if a direct relationship between methane migration, stream contamination, and air emissions exists at those sites. Our analysis indicates that subsurface methane migration, stream methane contamination, and air emissions might not be all present or detectable at a faulty/leaky shale gas well. Which of these signs of contamination, if any, exist is largely controlled by the local (hydro)geologic conditions. In each case, the most likely migration pathway was from gas charged zones up well annular spaces to confined permeable formations, then laterally to a direct discharge or by vertically controlled joints to streams, water wells, and the atmosphere. The confining units act as barriers to the buoyant movement of stray gases, allowing subsurface travel of gas for 1–4 km from a leaky gas well. The knowledge we learn from these three sites can guide the future investigations of methane contamination cases in other regions.