Regular observations of atmospheric mixing ratios of CO2 and CH4, combined with sodar measurements of the mixing layer height in the lower troposphere were used to assess night-time surface fluxes of these gases in the urban environment (Krakow, southern Poland). The measurements performed over the 4-yr period (May 2005–May 2009) revealed a distinct seasonality of surface night-time fluxes of CO2, with the minimum of ca. 2 mmol m−2 h−1 during winter months and the maximum of ca. 20 mmol m−2 h−1 observed during summer months. The observed seasonality was induced by the biospheric component (soil respiration) which dominates the measured surface CO2 fluxes during summer months. The surface fluxes of CH4 scatter between ca. 50 and 200 μmol m−2 h−1, without clear seasonal trend. Significant flux of CH4 into the atmosphere (mean value over the whole observation period equal to ca. 97 μmol m−2 h−1), indicates a presence of relatively strong methane source on the investigated area. This source is linked to methane leakages from the city gas distribution network.