We report results from the first 3 years (1999–2001) of long-term measurements of net ecosystem exchange (NEE) at an AmeriFlux site over a mixed hardwood forest in northern lower Michigan. The primary measurement methodology uses eddy covariance systems with closed-path infrared gas analyzers at two heights (46 and 34 m) above the forest (canopy height is ∼22 m). One objective is to contribute to a more firmly established methodology of estimating annual net ecosystem production (NEP), by systematically examining the consequences of several variations of criteria to identify periods of unreliable measurements, and to fill gaps in the data. We compared two methods to fill data gaps (about 30% of time in 1999) due to missing observations or rejected data after quality control; one using short-term ensemble averages of the daily course and the other by semiempirical parametric models based on relationships between ecosystem respiration and soil temperature and between gross ecosystem photosynthetic uptake and photosynthetically active radiation. The modeled estimates were also used to replace eddy covariance fluxes during periods of weak and/or poorly developed turbulence when eddy covariance measurements cannot be expected to represent the ecosystem exchange. Examination of the fractions of eddy covariance fluxes and storage change relative to the expected ecosystem respiration suggested a friction velocity (u*) of 0.35 m s−1 as the lower limit for the acceptance of micrometeorologically determined NEE for this site. The differences in estimated annual NEP due to different criteria of data acceptance, measurement height, or gap-filling strategies turned out to be at least as large as the interannual variations over the 3 years. After discussing various analysis strategies we conclude that the best estimate of annual NEP at our site is achieved by replacing data gaps and measurements in low-u* conditions at all times with site and period-specific parametric models, using the upper measurement level (about 2.1 canopy heights). These “best estimates” of annual NEP for 1999–2001 amounted to 170 (1999), 160 (2000), and 80 (2001) g C m−2. We also discuss some problems of assigning quantitative estimates of uncertainty for annual NEP.