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Elevated tritium, radiocarbon, Hg, and volatile organic compounds associated with low-level radioactive waste (LLRW) at the USGS Amargosa Desert Research Site (ADRS) have stimulated research on factors and processes that affect contaminant gas distribution and transport. Consequently, we examined the sources, mixing, and biogeochemistry of CO2 and CH4, two additional important species in the unsaturated zone at ADRS. In spring 2015 and 2016, shallow unsaturated zone gas samples were collected from the 1.5-m depth both inside and outside the LLRW disposal area. Samples also were collected from two 110-m-deep multi-level gas-sampling boreholes and a distant background site. These samples were analyzed for CO2 mole fraction (xCO(2)) and C isotopic composition (delta C-13-CO2) and CH4 mole fraction (xCH(4)). Graphical analysis of the results indicates mixing of CO2 characteristic of the root zone (delta C-13 -18 to -19 parts per thousand), deep soil gas of the capillary fringe (-13 to -15 parts per thousand), and CO2 produced by microbial respiration of organic matter disposed in the LLRW trenches ( 22 to -25 parts per thousand). Distribution of CH4 overall reflects atmospheric sources and production in anaerobic microzones in the LLRW area and methanotrophy in the undisturbed shallow subsurface outside the LLRW area. Although xCH(4) reflecting lateral transport from the LLRW area is decreasing with time in the deep profiles, deep unsaturated zone xCO(2) has changed little in recent decades. The results imply that CH4 and delta C-13-CO2 may serve as good tracers of anthropogenic effects in the unsaturated zone even when CO2 primarily reflects natural processes.