We measured the carbon isotopic composition of pore water carbon dioxide from Sallie’s Fen, a New Hampshire poor fen. The isotope profiles are used in combination with a one-dimensional diffusion–reaction model to calculate rates of methane production, oxidation and transport over an annual cycle. We show how the rates vary with depth over a seasonal cycle, with methane produced deeper during the winter months and at progressively shallower depths into the summer season. The rates of methane production, constrained by the measured δ13Cdic profiles, cannot explain high methane emission during the summer. We suggest that much of the methane produced during this time comes either from the unsaturated peat, or from the top 1–3 cm of saturated peat where episodic exchange with the atmosphere makes it invisible to our method.