This study investigated sources and sinks of methane (CH 4 ) and nitrous oxide (N 2 O) in the Brisbane River estuary, Australia. Field measurements and laboratory incubation experiments were performed to determine the contribution of the water column, sediments, influent creeks and discharge from a wastewater treatment plant, to greenhouse gas levels occurring in the estuary.Sampling was conducted at 16 sites along the estuary with more detailed studies at three of these sites, located in the lower, middle and upper estuarine reaches, respectively. The estuary is a source of CH 4 and N 2 O with their saturation in the surface water ranging between 2,160 and 26,900% for CH 4 , and between 140 and 230% for N 2 O, relative to their respective atmospheric concentrations. Estuarine sediments were identified as sources for both CH 4 and N 2 O, as concentrations for both dissolved gases were higher in the pore water at the sediment surfaces in comparison to the water column samples at all sites. Methane and N 2 O were produced in silty sediments as shown in sediment-water incubations. Creeks were detected to be a source of CH 4 and N 2 O, as their concentrations were higher in the creek in comparison to those measured at the confluence of the creek and the estuary. The estuarine water column was identified as a CH 4 sink; however, the water column was neither a sink nor a source for N 2 O. A wastewater treatment plant discharging effluent into the tributary did not contribute significantly to the creek CH 4 levels, but may have elevated N 2 O at the direct point of discharge. A budget estimate of the Brisbane River estuary showed that sediments are not the sole source of CH 4 , as the sediment-water fluxes are far less (1%) than what is consumed, emitted or transported to the ocean. An unknown CH 4 source is therefore likely present, which is yet to be revealed. In contrast, most of N 2 O produced in the estuarine sediments was emitted to the atmosphere.