AbstractUrban areas play an essential role in the global carbon balance, being responsible for more than 70% of anthropogenic carbon emissions, entering the atmosphere mainly in the form of carbon dioxide (CO2). Another crucial component of the carbon balance of the urban atmosphere is CO2 exchange with the biosphere, expressed in both emission and absorption fluxes. The biosphere component of the net CO2 flux is inseparably linked to the water (H2O) balance due to evapotranspiration. This article presents an estimation of CO2 and H2O net fluxes based on eddy covariance (EC) tower measurements and in‐depth analysis of its temporal and spatial variability for a typical urban site at mid‐latitude of the northern hemisphere. The source area was divided into two sectors, one representing dense urban development with sources of CO2 from traffic and households, and the second containing predominantly recreation and sports areas. Temporal variability analysis of evapotranspiration showed a clear seasonal cycle closely correlated with incoming radiation and air temperature, with the seasonal mean ranging from 0.4 mm·day−1 in winter to 1.6 mm·day−1 in summer. As a result of similar green coverage between the urban and green sectors, spatial variability was statistically insignificant. The net CO2 flux over a seasonal cycle was less pronounced for the total source area with a mean of 5.0 g C·m−2·day−1 in summer and 7.5 g C·m−2·day−1 in winter. However, significant variations between urban and green sectors were observed with the highest seasonal mean difference of 4.5 g C·m−2·day−1 in winter. The results confirm that while on the local, short time‐scale urban vegetation has a potential to mitigate the emissions, it is not able to offset them.