The decentralisation of wastewater treatment operations exposes several environmental consequences. This includes the fugitive emission of two greenhouse gases, nitrous oxide (N2O) and methane (CH4). The magnitude of these emissions is presently unclear. Therefore, it is necessary to measure the extent of the release of N2O and CH4 gas from decentralised wastewater treatment plants (WWTPs) in order to quantify the impact these emissions will have on the environment and to determine strategies to reduce them. Specifically, this pilot study employed an online non-dispersive infrared (NDIR) gas analyser and flux hood to evaluate the spatial and short-term temporal distribution of N2O and CH4 flux over half a day, from an aeration tank system within a decentralised sewage mining plant. The aeration tank system was able to emit N2O fluxes of up to 11.6 g N2O m−2 day−1 and CH4 fluxes of up to 1.1 g CH4 m−2 day−1. The N2O and CH4 fluxes varied rapidly over short time intervals in the same position (as high as 45% for N2O and 36% for CH4) and could almost triple in magnitude between two different positions across the surface of the aeration tank (within a distance no greater than 1.5 to 2 m).