Graduation date: 2007Many pesticides, polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and polycyclic aromatic hydrocarbons are persistent, bio-accumulative, and toxic. These semi-volatile organic compounds (SOCs) can undergo atmospheric transport and deposition in cold, remote ecosystems. A better understanding of their accumulation in the fish of these ecosystems is important to better predict the human and ecosystem health risks of these and other SOCs. This dissertation describes the development of analytical methods to measure 91 of these SOCs at concentrations <1 ng/g in fish tissues, and determination of fish and ecosystem characteristics affecting their distributions throughout western US lakes. To measure PBDEs in extracts, a gas chromatography low resolution mass spectrometric method was developed for the selective and quantitative isotope dilution analysis of 39 PBDEs. PBDE specific high mass ion production was optimized, selectivity enhanced, and accuracy was improved with the use of ¹³C surrogates. An analytical method was developed and validated to measure 91 target compounds at <1 ng/g in fish. The method was sensitive (0.2-990 pg/g detection limits), efficient (61 % recovery), reproducible (4.1 %RSD), and accurate (8 % deviation, NIST SRM #1946). SOC concentrations in 136 fish from 14 remote lakes were compared to human health contaminant screening values. Most fish concentrations were 1-6 orders of magnitude below screening values, however average fish concentrations of dieldrin and/or p,p’-DDE in 8 lakes exceeded lifetime cancer screening values for subsistence fishers. Because fish SOC concentrations varied several orders of magnitude within and between lakes, statistical models were developed to explain the influence of 7 fish and 12 ecosystem characteristics on fish SOC concentrations. Fish characteristics that best explained SOC concentrations were fish age and lipid concentration. Average air temperature, measured winter SOC deposition, and lake elevation were ecosystem characteristics that best explained fish concentrations of historic use pesticides, current use pesticides, and PCBs and PBDEs, respectively. This suggests that human health impacts are possible from some atmospherically deposited SOCs, and that fish SOC concentrations in western US lakes can be explained by combinations of fish lipid concentration and/or age, and air temperatures, elevations, proximity to sources, and/or winter SOC deposition.