We investigated the budget equations of H₂O and CO₂ exchanges in a hilly KoFlux forest catchment. This site is characterized by a rolling terrain and mountain-valley circulations. The field measurements included two-level eddy-covariance (at 20 and 40 m) and H₂O/CO₂ concentration profile systems on a single tower. To properly assess the vertical wind speed, we applied a planar fit rotation with atmospheric stabilities and wind directions. As atmospheric stability changed, the planar fit rotation gave different aspect slopes, which impacted on the estimation of vertical advection. Horizontal advection was estimated using a simple assumption of the quadratic profile within a forest canopy. Our analysis shows that the contributions of advective components were different not only between the two levels but also between CO₂ and H₂O. At 40 m, the vertical and horizontal advection canceled each other out and therefore the turbulent eddy flux alone can be used for net ecosystem exchanges within 10% uncertainty. Near the canopy top (at 20 m), however, vertical advection should be taken into account for CO₂. Also, even in windy conditions, advective fluxes were substantial. Well-calibrated multi-level eddy-covariance measurements along with profile measurement may provide useful insights for estimating the magnitude of advective fluxes over heterogeneous land surfaces.