The effect of locally generated circulation from a clearcut formed by forest management practices on eddy covariance fluxes, over an otherwise homogeneous forest canopy, are discussed. The clearcut is located nearly 500 meters from the eddy covariance tower and has length wise extension of 1 km and maximum width 300 m. Eddy covariance CO2, water vapor and sensible heat flux measurements over a 11 year old 11 m tall slash pine canopy are analyzed by classifying the data with respect to the prevailing wind directions. The measured fluxes, concentrations and standard deviations of the scalar quantities are compared for different days with advective and non-advective wind directions. Results suggest that horizontal and vertical advection from the clearcut introduces significant differences in the measured fluxes when compared to the observations during non-advective wind directions. Various turbulence quantities measured using a vertical array of sonic anemometers within and above the canopy are also presented to substantiate the findings on the fluxes and to illustrate the features of advection.