Soil CO 2 and O 2 cycles are coupled in some processes (e.g., respiration) but uncoupled in others (e.g., silicate weathering). One benchmark for interpreting soil biogeochemical processes affected by soil pCO 2 and pO 2 is to calculate the apparent respiratory quotient (ARQ). When aerobic respiration and diffusion are the dominant controls on gas concentrations, ARQ equals 1; ARQ deviates from 1 when other processes dominate soil CO 2 and O 2 chemistry. Here, we used ARQ to understand lithologic, hillslope, and seasonal controls on soil gases at the Susquehanna Shale Hills Critical Zone Observatory in central Pennsylvania. We measured soil pCO 2 and pO 2 at three depths from the soil surface to bedrock across catenas in one shale and one sandstone watershed over three growing seasons. We found that both parent lithology and hillslope position significantly affect soil gas concentrations and ARQ. Soil pCO 2 was highest (>5%) and pO 2 was lowest (<16%) in the valley floors. Controlling for depth, pCO 2 was higher and pO 2 was lower across all sites in the sandstone watershed. We attribute this pattern to higher macroporosity in sandstone lithologies, which results in greater root respiration at depth. We recorded seasonal variation in ARQ at all sites, with ARQ rising above 1 during July through September, and dipping below 1 in the early spring. We hypothesize that this seasonal fluctuation arises from anaerobic respiration in reducing microsites July through September when the soils are wet and demand for O 2 is high, followed by oxidation of reduced species when the soils drain and re‐oxygenate. We estimate that this anaerobic respiration in microsites contributes 36 g C m−2 yr−1 to the soil C flux. Our results provide evidence for a conceptual model of metal cycling in temperate watersheds and point to the importance of anaerobic respiration to the carbon flux from forest soils.