The dataset consists of a continuous time series of heat (latent and sensible) and trace gas (carbon dioxide and methane) fluxes obtained by eddy-covariance, gas concentrations and some ancillary meteorological data (e.g. air temperature, relative humidity, pressure, photosynthetically active radiation, total incoming radiation, wind speed and direction). The data were collected at Nxaraga, on the south edge of Chief’s Island (19°32'53''S; 23°10'45'E), in the seasonally flooded area of the Okavango Delta, Botswana, for the purpose of quantifying greenhouse gas fluxes from seasonal floodplains. The data is reported at half-hourly interval for the measurement period 01/01/2018 to 31/12/2020. Missing data were caused by instrumentation downtime and are reported as -9999.