The quantification of greenhouse gas sources and sinks is important to understanding the impact of climate change. Methane (CH4) is a potent greenhouse gas, which, on a global scale, is released largely as a product of anaerobic microbial decomposition and predominantly from wetlands. A zone of intense CH4 production just below the water table is thought to contribute significantly to the overall flux from peat bogs. We describe the use of membrane inlet quadrupole mass spectrometry (QMS) to confirm the existence of bubbles, their gaseous concentrations and their localization at a fine spatial resolution within intact peat cores. We use the distribution of the noble gas argon (Ar) and the distinct QMS responses to dissolved and gaseous (bubble) phases to identify trapped bubbles with a resolution of 0.6 mm. Bubbles with CH4 concentrations of up to 20 kPa were widely distributed in the upper 300 mm of the cores with ∼11% of all profiles comprising bubbles. The dissolved concentrations responsible for the bubbles were on average 83±80 μm, indicating lower concentrations relative to other QMS studies. We suggest that if the distinction between dissolved and gaseous phases is not made in studies of CH4 within peat profiles then the prominence of bubbles is likely to result in overestimates of dissolved CH4 concentrations. Fluxes of CH4 from peat as a result of drawdown or other perturbation are likely to be large, rapid and short lived because of bubble burst, and also larger than from peat without bubbles. We suggest that the dynamics of fluxes need to be modelled taking into account both gaseous and dissolved phases. Estimates of potential fluxes that assume CH4 is dissolved are likely to overestimate fluxes if the gaseous phase has not been taken into account.