The Marcellus Shale Region is found along the east coast and covers most of PA. This region has been greatly affected by hydraulic fracturing (HF), or fracking, which is a method that is widely used to obtain natural gas. The waste from fracking is released into surrounding waters, affecting ecosystem health. To understand the effects of fracking on organisms, brook trout (Salvelinus fontinalis) were divided into three treatment groups and exposed to varying concentrations of surrogate HF wastewater. RNAseq analyses were carried out to assess changes in gene expression in S. fontinalis over 2 weeks of exposure. Differentially expressed isoforms were identified for several transcripts and genes from two broad functional groups: genes that affected metal ion binding and genes that affected the physical condition of the fish. This furthers our understanding of how environmental pollutants affect fish at the molecular level.