Abstract. A severe reduction of greenhouse gas emissions is necessary to reach the objectives of the Paris Agreement. The implementation and continuous evaluation of mitigation measures requires regular independent information on emissions of the two main anthropogenic greenhouse gases, carbon dioxide (CO2) and methane (CH4). Our aim is to employ an observation-based method to determine regional-scale greenhouse gas emission estimates with high accuracy. We use aircraft- and ground-based in situ observations of CH4, CO2, carbon monoxide (CO), and wind speed from two research flights over the Upper Silesian Coal Basin (USCB), Poland, in summer 2018. The flights were performed as a part of the Carbon Dioxide and Methane (CoMet) mission above this European CH4 emission hot spot region. A kriging algorithm interpolates the observed concentrations between the downwind transects of the trace gas plume and then the mass flux through this plane is calculated. Finally, statistic and systematic uncertainties are calculated from measurement uncertainties and through several sensitivity tests, respectively. For the two selected flights, the in situ derived annual CH4 emission estimates are 13.8 ± 3.6 kg/s and 15.1 ± 3.0 kg/s, which is well within the range of emission inventories. The regional emission estimates of CO2, which were determined to be 1.21 ± 0.72 t/s and 1.12 ± 0.37 t/s, are in the lower range of emission inventories. CO mass balance emissions of 10.1 ± 3.2 kg/s and 10.7 ± 2.9 kg/s for the USCB are slightly higher than the emission inventory values. The CH4 emission estimate has a relative error of 21–26 %, the CO2 estimate of 33–60 %, and the CO estimate of 27–32 %. These errors mainly result from the uncertainty of atmospheric background mole fractions and the changing planetary boundary layer height during the morning flight. In the case of CO2, biospheric fluxes also add to the uncertainty and hamper the assessment of emission inventories. These emission estimates characterize the USCB and help to verify emission inventories and develop climate mitigation strategies.