The role of mid-latitude forests in the sequestration of carbon (C) is of interest to an increasing number of scientists and policy-makers alike. Net CO2 exchange can be estimated on an annual basis, using eddy-covariance techniques or from ecological inventories of C fluxes to and from a forest. Here we present an intercomparison of annual estimates of C exchange in a mixed hardwood forest in the Morgan-Monroe State Forest, Indiana, USA for two years, 1998 and 1999. Based on eddy-covariance measurements made at 1.8 times canopy height from a tower, C uptake by the forest was 237 and 287 g C m−2 y−1 for 1998 and 1999, respectively. For the same time period, biometric and ecophysiological measures and modelled estimates of all significant carbon fluxes within deciduous forests were made, including: change in living biomass, aboveground and belowground detritus production, foliage consumption, and forest floor and soil respiration. Using this ecological inventory method for these same two time periods, C uptake was estimated to be 271 and 377 g C m−2 y−1, which are 14.3% and 31.4% larger, respectively, than the tower-based values. The relative change between this method’s annual estimates is consistent with that of the eddy-covariance based values. Our results indicate that the difference in annual C exchange rates was due to reduced heterotrophic soil respiration in 1999.