The Crop Wind-Energy Experiment (CWEX) provides a platform to investigate the effect of wind turbines and large wind farms on surface fluxes of momentum, heat, moisture, and carbon dioxide (CO2). In 2010 and 2011, eddy covariance flux stations were installed between two lines of turbines at the southwest edge of a large Iowa wind farm from late June to early September. We report changes in fluxes of momentum, sensible heat, latent heat, and CO2 above a corn canopy after surface air had passed through a single line of turbines. In 2010, our flux stations were placed within a field with homogeneous land management practices (same tillage, cultivar, chemical treatments). We stratify the data according to wind direction, diurnal condition, and turbine operational status. Within these categories, the downwind–upwind flux differences quantify turbine influences at the crop surface. Flux differences were negligible in both westerly wind conditions and when the turbines were non operational. When the flow is perpendicular (southerly) or slightly oblique (southwesterly) to the row of turbines during the day, fluxes of CO2 and water (H2O) are enhanced by a factor of five in the lee of the turbines (from three to five turbine diameter distances downwind from the tower) as compared to a west wind. However, we observe a smaller CO2 flux increase of 30–40% for these same wind directions when the turbines are off. In the nighttime, there is strong statistical significance that turbine wakes enhance upward CO2 fluxes and entrain sensible heat toward the crop. The direction of the scalar flux perturbation seems closely associated to the differences in canopy friction velocity. Spectra and co-spectra of momentum components and co-spectra of heat also demonstrate nighttime influence of the wind turbine turbulence at the downwind station.