The Mer Bleue peatland is a large ombrotrophic bog with hummock-lawn microtopography, poor fen sections and beaver ponds at the margin. Average growing-season (May–October) fluxes of methane (CH₄) measured in 2002–2003 across the bog ranged from less than 5 mg m⁻² d⁻¹ in hummocks, to greater than 100 mg m⁻² d⁻¹ in lawns and ponds. The average position of the water table explained about half of the variation in the season average CH₄ fluxes, similar to that observed in many other peatlands in Canada and elsewhere. The flux varied most when the water table position ranged between −15 and −40 cm. To better establish the factors that influence this variability, we measured CH₄ flux at approximately weekly intervals from May to November for 5 years (2004–2008) at 12 collars representing the water table and vegetation variations typical of the peatland. Over the snow-free season, peat temperature is the dominant correlate and the difference among the collars’ seasonal average CH₄ flux is partially dependent on water table position. A third important correlate on CH₄ flux is vegetation, particularly the presence of Eriophorum vaginatum, which increases CH₄ flux, as well as differences in the potential of the peat profile to produce and consume CH₄ under anaerobic and aerobic conditions. The combination of peat temperature and water table position with vegetation cover was able to explain approximately 44% of the variation in daily CH₄ flux, based on 1097 individual measurements. There was considerable inter-annual variation in fluxes, associated with varying peat thermal and water table regimes in response to variations in weather, but also by variations in the water level in peripheral ponds, associated with beaver dam activity. Raised water level in the beaver ponds led to higher water tables and increased CH₄ emission in the peatland.