Multi-layer Lagrangian models could be useful techniques for studying stable isotope exchange within and just above plant canopies. The main objective of this study was to evaluate the use of an analytical Lagrangian analysis (localized near-field theory, LNF), to study 13CO2 and C18OO isotope exchange in different plant canopies by comparing the LNF estimates with those provided by the eddy covariance (EC) technique and the isotope flux ratio method (IFR). Mixing ratios of stable isotopes of CO2 were measured within and above a temperate deciduous forest, tallgrass prairie and corn field using a multi-port sampling system and the tunable diode laser spectroscopy technique. Wind velocity data and the net CO2 ecosystem exchange (NEE) were measured above the plant canopies using an EC system. The wind velocity data and CO2 stable isotope mixing ratios were combined with the LNF theory to infer NEE and source/sinks of isotopes inside canopies. The LNF NEE estimates were likely affected by the flux decoupling in the forest canopy, resulting in a low correlation (R2 ranging from 0.03 to 0.35) between LNF and EC NEE estimates. On the other hand, LNF NEE estimates for corn and grassland canopies showed better correlation with EC NEE estimates (R2 ranging from 0.58 to 0.85), suggesting better coupling between in and above canopy air flows. Although, both LNF and IFR estimates showed large variability, our results show that the LNF approach reduced the uncertainties of the isotope compositions of NEE when compared to the IFR approach. These results suggest that LNF is a useful tool to study CO2 isotope exchange within short canopies where flux measurements are more challenging than inside tall canopies.