An assessment of observed vertical flux divergence in long-term eddy-covariance measurements over two Midwestern forest ecosystems

Vertical divergence of CO 2 fluxes is observed over two Midwestern AmeriFlux forest sites. The differences in ensemble averaged hourly CO 2 fluxes measured at two heights above canopy are relatively small (0.2–0.5 μmol m −2 s −1), but they are the major contributors to differences (76–256 g C m −2 or 41.8–50.6%) in estimated annual net ecosystem exchange (NEE) in 2001. A friction velocity criterion is used in these estimates but mean flow advection is not accounted for. This study examines the effects of coordinate rotation, averaging time period, sampling frequency and co-spectral correction on CO 2 fluxes measured at a single height, and on vertical flux differences measured between two heights. Both the offset in measured vertical velocity and the downflow/upflow caused by supporting tower structures in upwind directions lead to systematic over- or under-estimates of fluxes measured at a single height. An offset of 1 cm s −1 and an upflow/downflow of 1° lead to 1% and 5.6% differences in momentum fluxes and nighttime sensible heat and CO 2 fluxes, respectively, but only 0.5% and 2.8% differences in daytime sensible heat and CO 2 fluxes. The sign and magnitude of both offset and upflow/downflow angle vary between sonic anemometers at two measurement heights. This introduces a systematic and large bias in vertical flux differences if these effects are not corrected in the coordinate rotation. A 1 h averaging time period is shown to be appropriate for the two sites. In the daytime, the absolute magnitudes of co-spectra decrease with height in the natural frequencies of 0.02–0.1 Hz but increase in the lower frequencies (