The effects of different averaging operators and atmospheric stability on the turbulent fluxes are investigated using the vertical velocity, air temperature, carbon dioxide concentration, and absolute humidity data measured at 10 Hz by a 3-dimensional sonic anemometer and an open-path $CO_2/H_2O$ infrared gas analyzer installed at a height of 18.5 m on the rooftop of the Jungnang KT building located at a typical residential area in Seoul, Korea. For this purpose, 7 different averaging operators including block average, linear regression, and moving averages during 100 s, 300 s, 600 s, 900 s, and 1800 s are considered and the data quality control procedure such as physical limit check and spike removal is also applied. It is found that as the averaging interval becomes shorter, turbulent fluxes computed by the moving average become smaller and the ratios of turbulent fluxes computed by the 100 s moving average to the fluxes by the 1800 s moving average under unstable stability are smaller than those under neutral stability. The turbulent fluxes computed by the linear regression are 85~92% of those computed by the 1800 s moving average and nearly the same as those computed by 900 s moving average, implying that the adequate selection of an averaging operator and its interval will be very important to estimate more accurate turbulent fluxes at urban area.