Methane emissions were measured from a bog and lake in the Experimental Lakes Area in Northern Ontario in 1992 and 1993, prior to and following flooding. Bog fluxes were small in 1992 (0.27 mg m −2 d −1) but increased 5-fold in 1993 after flooding. Over the bog, there was a diel cycle of nighttime emission and daytime uptake in 1992 in contrast to constant emission in 1993. Lake emissions decreased after flooding but were much greater than bog emissions in both years (average = 7.3 mg m −2 d −1). Seasonally, the bog flux was correlated with ground temperatures after flooding. In 1992, lake fluxes were correlated with air temperature on a daily basis. In contrast, seasonal lake fluxes were correlated with water and sediment temperatures in 1992, but only with sediment temperatures in 1993. These results are explained with respect to the effects of flooding on lake and bog dynamics.