Cotter Dam (Canberra, Australia), built in 1912 and enlarged to its current size (4 GL) in 1951, is a water supply reservoir that has recently been enlarged again (to 80 GL) to increase water security. Vegetation consists mainly of regrowth Pinus radiata and scrubby bushland as the catchment recovers from a devastating fire in 2003. Floating chamber measurements of CO2 and CH4 fluxes using a Picarro 1301 CRDS have been undertaken to provide baseline data against which future GHG emissions can be compared as the dam fills and new soil and vegetation are inundated. Drought-breaking rains led to heavy flooding with more than 80 GL passing through the reservoir during a two-month period. Areal mean CH4 emissions from the reservoir prior to the flooding were low (0.26 ± 0.14 mmol m-2 d-1), relatively uniform across the 8 measurement sites, and therefore typical of 'mature' reservoirs. Following the flood, the mean reservoir CH4 emission increased to 6.2 ± 1.4 mmol m-2 d-1 with emissions at the upstream end of the reservoir (the deposition zone) approximately 100 times greater (31 ± 7.6 mmol m-2 d-1) than emissions near the dam wall (0.28 ± 0.019 mmol m-2 d-1), a pattern we consistently observed in two other reservoirs in much wetter and more densely vegetated southeast Queensland. Over the following year, there has been a return to more normal runoff conditions, mean emissions have fallen to 2.0 ± 0.75 mmol m-2 d-1 and the spatial gradient in emissions has weakened.