Methodology for determining fluxes of CO2 and H2O vapor with the eddy-covariance method using data from instruments on a 447-m tower in the forest of northern Wisconsin is addressed. The primary goal of this study is the validation of the methods used to determine the net ecosystem exchange of CO2. Two-day least squares fits coupled with 30-day running averages limit calibration error of infrared gas analyzers for CO2 and H2O signals to ≈2%–3%. Sonic anemometers are aligned with local streamlines by fitting a sine function to tilt and wind direction averages, and fitting a third-order polynomial to the residual. Lag times are determined by selecting the peak in lagged covariance with an error of ≈1.5%–2% for CO2 and ≈1% for H2O vapor. Theory and a spectral fit method allow determination of the underestimation in CO2 flux (<5% daytime, <12% nighttime) and H2O vapor flux (<21%), which is due to spectral degradation induced by long air-sampling tubes. Scale analysis finds 0.5-h flux averaging periods are sufficient to measure all flux scales at 30-m height, but 1 h is necessary at higher levels, and random errors in the flux measurements due to limited sampling of atmospheric turbulence are fairly large (≈15%–20% for CO2 and ≈20%–40% for H2O vapor at lower levels for a 1-h period).