Abstract. The eddy covariance (EC) technique is the most direct method for measuring the exchange between the surface and the atmosphere in different ecosystems. Thus, it is commonly used to get information on air pollutant and greenhouse gas emissions, and on turbulent heat transfer. Typically an ecosystem is monitored by only one single EC measurement station at a time, making the ecosystem-level flux values subject to random and systematic uncertainties. Furthermore, in urban ecosystems we often have no choice but to conduct the single-point measurements in non-ideal locations such as close to buildings and/or in the roughness sublayer, bringing further complications to data analysis and flux estimations. In order to tackle the question of how representative a single EC measurement point in an urban area can be, two identical EC systems – measuring momentum, sensible and latent heat, and carbon dioxide fluxes – were installed on each side of the same building structure in central Helsinki, Finland, during July 2013–September 2015. The main interests were to understand the sensitivity of the vertical fluxes on the single measurement point and to estimate the systematic uncertainty in annual cumulative values due to missing data if certain, relatively wide, flow-distorted wind sectors are disregarded. The momentum and measured scalar fluxes respond very differently to the distortion caused by the building structure. The momentum flux is the most sensitive to the measurement location, whereas scalar fluxes are less impacted. The flow distortion areas of the two EC systems (40–150 and 230–340∘) are best detected from the mean-wind-normalised turbulent kinetic energy, and outside these areas the median relative random uncertainties of the studied fluxes measured by one system are between 12 % and 28 %. Different gap-filling methods with which to yield annual cumulative fluxes show how using data from a single EC measurement point can cause up to a 12 % (480 g C m−2) underestimation in the cumulative carbon fluxes as compared to combined data from the two systems. Combining the data from two EC systems also increases the fraction of usable half-hourly carbon fluxes from 45 % to 69 % at the annual level. For sensible and latent heat, the respective underestimations are up to 5 % and 8 % (0.094 and 0.069 TJ m−2). The obtained random and systematic uncertainties are in the same range as observed in vegetated ecosystems. We also show how the commonly used data flagging criteria in natural ecosystems, kurtosis and skewness, are not necessarily suitable for filtering out data in a densely built urban environment. The results show how the single measurement system can be used to derive representative flux values for central Helsinki, but the addition of second system to other side of the building structure decreases the systematic uncertainties. Comparable results can be expected in similarly dense city locations where no large directional deviations in the source area are seen. In general, the obtained results will aid the scientific community by providing information about the sensitivity of EC measurements and their quality flagging in urban areas.