This dataset contains three types of observations carried out within the CoCO2 project: A: Urban ecosystem flux time series The urban ecosystem flux tower is installed on the roof of the Faculty of Physics and Applied Computer Science building. The elevation of instruments installed on the top of the tower is approximately 40 m.a.g.l. The measurement system consists of a Gill Windmaster sonic anemometer, LICOR LI7500DS open path CO2/H2O analyser, a Huxeflux NR01 net radiometer, and a SmartFlux 3 datalogger. It is supplemented by a VAISALA WXT520 combined weather station delivering Biomet data for the system. B: Vertical profiles of the CO2 and CH4 mixing ratios from the Krakow urban area Vertical profiles of CO2 and CH4 within the urban boundary layer of Krakow city were performed using two different platforms. The first platform was a tethered touristic balloon operated by the Balon Widokowy Sp. z o.o. company in the city centre. C: Diurnal variability of the isotopic composition of atmospheric CO2 The last part of the data set contains the isotopic analysis of flask samples collected every 4 hours during flight campaigns. Each sample was collected using an automatic flask sampler (shown in Fig. 9) in pair of glass flasks (1 l and 3 l capacity) by flushing with dry air. The air inlet was installed on the roof of Faculty building ca. 25 m a.g.l