Perfluorinated alkyl substances (PFAS) are synthetic organic molecules with straight or branched carbon chains bonded to fluorine atoms. Recent studies have shown various adverse health effects (cancer, birth defects, estrogen inhibition) via exposure to PFAS, e.g. drinking water from the Great Lakes, despite its extensive usage in firefighting foams, non-stick cookware, and pesticides. The Great Lakes Ecosystem is a home to a wide variety of unique fish species and it is unknown how they are being affected by these substances. A molecular level study offers an approach to identify how various PFAS molecules are binding to proteins that belong to Great Lakes benthic species in an efficient manner. In this study, the Molecular Operating Environment (MOE) software package has been used to find potential PFAS binding sites for protein receptors. These binding sites were then examined with a large database of PFAS molecules through docking, molecular dynamic simulations, and binding free energy calculations using end state approaches. The calculated binding free energies provide insight towards understanding the binding behavior of PFAS to proteins as well as its effect on the Great Lakes ecosystem.