This study reports recent developments in mulitlayer turbulent transport methods to compute distributions of strengths of scalar sources and sinks Sc as well as turbulent fluxes Fc within the plant–atmosphere continuum. In particular, we focus on the so-called “inverse methods” that estimate Sc from measured mean scalar concentration (or temperature) distribution within the canopy without resorting to any ecophysiologically based input. These approaches are able to reproduce measured turbulent fluxes above and within the canopy without relying on gradient diffusion formulation. Comparison between measured and modeled sensible heat flux vertical attenuation within the canopy suggests that all three methods provided comparable root-mean squared error (RMSE) (∼50 W m−2). Furthermore, correcting for local atmospheric stability significantly improved the agreement between model calculations and measurements. Comparisons between measured and modeled land surface fluxes of sensible heat, latent heat, and CO2 above the canopy are conducted using wavelet spectral methods applied to a wide range of temporal scales (30 min–2 yr). This study is the first to rigorously assess the performance of several inverse methods for such a broad range of time scales. We found that the three inverse modeled flux spectra bound the measured one. Hence, spectral agreement among the three models provides the necessary confidence in calculated fluxes and scalar sources. Conversely, large disagreement between the inverse models “flags” large uncertainties at those particular time scales.