An accurate determination of turbulent fluxes over an urban area is a challenging task due to its morphological diversity and associated flow complexity. In this study, an eddy covariance (EC) method is applied over a highly heterogeneous urban area in a small city (Gongju), South Korea to investigate the quantitative influence of 'coordinate tilt' in determining the turbulent fluxes of sensible heat, latent heat, momentum, and carbon dioxide mass. Two widely-used coordinate transform methods are adopted and applied to eight directional sections centered on the site to analyze a 1-year period EC measurement obtained from the urban site: double rotation (DR) and planar fit (PF) transform. The results show that mean streamline planes determined by the PF method are distinguished from the sections, representing morphological heterogeneity of the site. The sectional pitch angles determined by the DR method also compare well with those in the PF method. Both the PF and DR methods show large variabilities in the determined streamline planes at each directional section, implying that flow patterns may form in a complicate way due to the surface heterogeneity. Resulting relative differences of the turbulent fluxes, defined by (F DR -F PF )/F DR , are found on average +13% in sensible heat flux, +21% in latent heat flux, +37% in momentum flux, and +26% in carbon dioxide mass flux, which are larger values than those reported previously for fairly homogeneous natural sites. The fractional differences depend significantly on wind direction, showing larger differences in northerly winds at the measurement site. It is also found that the relative fractional differences are negatively correlated with the mean wind speed at both stable/unstable atmospheric conditions. These results imply that EC turbulent fluxes determined over heterogeneous urban areas should be carefully interpreted with considering the uncertainty due to 'coordinate tilt' effect in their applications.