CO2 fluxes for six stand types are inferred by decomposing eddy-covariance (EC) fluxes measured at a 447-m tower using footprint models and ecosystem models in a case study. The functional parameters in the ecosystem models are estimated for each stand type utilizing temporal EC flux series. The results show differences in terms of the functional parameters and fluxes among the different stand types that are consistent with general expectations for the respective stand types. The fluxes, in addition to measurements at two nearby short towers, are used for flux aggregation in the region. Comparisons suggest that it is critical for flux aggregation to distinguish the wetland from the upland. A distinction among three upland forests and between forested and lowland wetlands could be important, too. The difference in aggregated values of net ecosystem-atmospheric exchange of CO2 with the watershed function classification scheme and with the stand-type level classification scheme can reach about 250 gC m−2 season−1 over the entire growing season. Analyses suggest that the six-stand classification scheme still does not capture all the variability in stand characteristics relevant to CO2 exchange. In addition, the varying fluxes for the same stand type with location in the region challenge the widely used land-cover-based ecosystem classification scheme. It is improper to use EC measurements at any single tower to approximate CO2 fluxes in the region. Implications may help identify key ecosystem types and design more measurements in the region. Limitations and future efforts are discussed.