<p>We report on two years of continuous monitoring of methane (CH<sub>4</sub>) and carbon dioxide (CO<sub>2</sub>) emissions at two contrasting sites in the Okavango Delta, North-Western Botswana, an inland delta bordered by the Kalahari Desert. Approximately 60% of the annual water influx into the Okavango Delta results from seasonal river discharges originating in the Angolan Highlands, and the remainder comes from direct rainfall. 96-98% of the 16.1 billion m<sup>3</sup> entering the Delta annually are lost through evapo-transpiration (1500 mm.year<sup>-1</sup>). Flooding is gradual and it takes the pulsed influx ca. 4-5 months to travel the 250 km separating the inlet in Mohembo from the main outlet in Maun. The wetlands of the Okavango Delta are in pristine condition and can be separated into three categories: permanently flooded, seasonally flooded (3-6 months per year) and occasionally flooded (typically once per decade).&#160;</p><p>Two eddy-covariance systems were set up in August 2017, one at Guma Lagoon (18&#176;57'53.01" S;&#160; 22&#176;22'16.20" E) at the edge of an extensive papyrus bed in the permanently-flooded section of the delta, and the second one at Nxaraga on the SW edge of Chief&#8217;s Island (19&#176;32'53'' S; 23&#176;10'45'' E) in the seasonal floodplain. In addition, monthly measurements of methane and carbon dioxide fluxes were taken using a clear dynamic chamber at the Nxaraga site along transects chosen to span the natural soil moisture gradient (very dry to waterlogged soils).</p><p>The emissions of methane exhibited contrasting spatial and temporal patterns between sites. At the seasonal wetland, very low fluxes of CH<sub>4</sub> were typically observed from January to June. Emissions increased abruptly from July-August onwards after flood waters rewetted the flooplain in that area of the Delta. Throughout the year, local emission hotspots of CH<sub>4</sub> were observed along the vegetated river channels within the flux footprint of the eddy-covariance system, whereas CH<sub>4</sub> oxidation was recorded in persistently dry areas where the soil is sandy and salt-crusted. The chamber measurements corroborated the findings of the eddy-covariance measurements and soil moisture is likely the dominant control of methane fluxes at the seasonal wetland.</p><p>The methane emissions from the floating papyrus mat in the permanent wetland exhibited a marked seasonal cycle, characterised by relatively high emissions (of the order of 250 nmol.m<sup>-2</sup>.s<sup>-1</sup>; 2.5 larger than peak emissions recorded at the seasonal wetland) in the summer months (November-March) and minimum emissions in winter (typically 50 nmol.m<sup>-2</sup>.s<sup>-1</sup> in June-August). At the seasonal timescale, methane emissions were strongly correlated to the phenological cycle of papyrus (lowest emissions during the senescence phase), suggesting that plant-mediated transport is the dominant control. The annual budgets of CH<sub>4</sub> and CO<sub>2</sub> in the permanent wetland were estimated at 153.4 &#177; 27.9 tons.km<sup>-2</sup> (3835.0 &#177; 697.5 CO<sub>2</sub>-eq) and -874.0 &#177; 200.4 tons.km<sup>-2</sup> respectively, making the permanent wetland a potent net source of carbon to the atmosphere.</p>