In efforts to understand the potential impacts of the Marcellus Shale extraction activities on stream health, we performed a baseline study on a focal pair of small streams in the Tenmile Creek watershed in Greene County, Pennsylvania. Bates Fork had intensive Marcellus Shale well drilling activity and several violations upstream from our study site. A tributary, Fonner Run, served as a control stream site with no drilling activity. Through two years of monitoring, we established baselines for water chemistry and biological communities of bacteria, fish and salamanders. In addition, we compared population genetic diversity of two darter species with microsatellite markers. Although no conclusive differences were found between the stream-pair, we established baseline parameters and gained insight into refining tools to detect the signature of Marcellus Shale extraction impacts on small streams in southwestern Pennsylvania. We conclude this chapter with lessons learned from this case study, future directions and suggestions for improved monitoring and detection of Marcellus Shale impacts on streams in southwestern Pennsylvania.