Persistent and bioaccumulative pollutants (PBPs) are continually introduced into the environment as a part of the massive ongoing chemical production that began several decades ago. The PBPs include several chemical families such as: industrial compounds, personal care products, agricultural chemicals, and pharmaceuticals. Most of these PBPs are neutral and more than 60% of them are halogenated. However the concentration distributions in the environment, partitioning properties, and environmental fate and behavior of many PBPs have not been investigated . Recent studies have reported on the lack of information regarding the occurrence, fate, and behavior of these PBPs in the environment (Howard and Muir 2006, 2010 and 2013). The authors emphasized the need for measurements of these PBPs in different environmental compartments in order to better understand their environmental fate and behavior. In this thesis, I investigated the occurrence of legacy and novel PBPs in a deep aquatic system, Lake Geneva. Measuring these compounds in environmental samples is a challenging task due to their trace level concentrations and due to the complexity of the samples, manifest as matrix effect. I employed comprehensive two-dimensional gas chromatography (GC×GC) to tackle these challenges. Throughout the thesis I refer to "novel PBPs" as PBPs that are neutral, organic, non-legacy, and that have not been measured in the environment. This terminology is similar to that adopted by Howard and Muir, 2010. I report results for several water column and sediment samples that were analyzed for a suite of 69 PBPs, including novel PBPs, PBDEs, PCBs, OCPs and halogenated benzenes. This leads to the first reported detection and quantification for several novel PBPs (i.e. 4-bromobiphenyl (4BBP), tribromobenzene (TBB), and pentachlorothiophenol (PCTP)) in a lake environment. Results for several legacy PBPs, including PBDEs and PCBs, are also reported. In Chapter 2 of the thesis I developed an analytical protocol for detection, quantification, and identity confirmation of trace level PBPs in environmental samples. This method took advantage of the separation power of GC×GC combined to highly sensitive detectors, including electron capture negative chemical ionization (ENCI)-TOFMS, micro electron capture detector (¿ECD), and flame ionization detector (FID). Chapter 2 evaluates the effectiveness of the application of GC×GC-ECD for the detection and quantification of trace-level PBPs in the lake environment. In particular, I investigate automated baseline correction and peak delineation algorithms for their ability to remove matrix effect and quantify trace level PBPs in complex environmental samples. By employing a suite of chemometric tests, I systematically assessed different baseline correction and peak delineation algorithms for their confidence and accuracy of target analyte quantification. The results of chemometric tests showed the crucial importance of the baseline correction algorithm for accurate peak integration. An aggressive baseline correction method systematically produced the best results for the chemometric tests, which indicated a better matrix effect removal. The results of the analytical protocol were also validated using a certified reference material. The validated analytical procedure led to the successful detection and quantification of 18 trace level target analytes, including 7 PAHs in a light diesel fuel and 11 chlorinated hydrocarbons.