This study is part of an inter-laboratory collaborating project led by the Environmental Protection Agency (EPA). The EPA provided water samples collected from a river, effluent of wastewater treatment plant (WWTP) and water treatment plant (WTP) in northeastern United States that uses chlorine disinfection. Non-targeted analysis was utilized to screen for a wide range of chemicals. The samples were prepared by solid-phase extraction (SPE) using Oasis HLB and analyzed by comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC/TOF-MS) in non-targeted analytical manner. By using non-targeted analysis, chemicals not targeted can be screened, while a targeted analysis analyzes known chemicals in a sample leaving unknown chemicals undetected. In this study, true detection of a chemical was determined by meeting the following criteria: it must be found only in the sample, must not be found in any field blank sample, and must have a mass spectral similarity score of 500 (50%) or above using the NIST mass spectral library. Data analysis was done by using the instrument software, ChromaTOF, and its add-in feature, “Statistical Compare”. After the automatic data analysis, manual review followed. In total, 382 unique compounds were identified from all six sample locations collected. After manual review, 135 compounds showed high similarity with the NIST mass spectra, and 247 were deemed as low identified compounds. In the wastewater effluent, a majority of the compounds were ingredients of pharmaceutical and personal care products (PPCPs) and flavoring/food additives. In the treated drinking water, 6 disinfection byproducts (DBPs) were detected and not detected in the feed water to the drinking water facility, but produced after treatment. Possible sources of the trace chemicals were discussed. Of all the chemicals tentatively identified, only two from the treated drinking water sample, tribromoacetic acid and dibromochloromethane are regulated in drinking water. This study confirms previous findings that PPCPs and DBPs continue to be pollutants of source waters. Also, the results indicate that non-target analysis was useful to evaluate the efficiency of wastewater and drinking water processes. Further study requires confirmation of the tentatively identified compound, quantification of the compounds for risk assessment and source investigation. The CD-ROM, an appendix to this thesis, is available for viewing at the Media Center in the SDSU Library.