The interaction between terrestrial ecosystems and the atmosphere continues to be a central research theme within climate, hydrology, and ecology communities. This interest is stimulated by research issues pertinent to both the fundamental laws and the hierarchy of scales. To further explorer such topics over various spatial and temporal domains, in this study, biosphere-atmosphere interactions are studied at two different scales, leaf-to-canopy and canopy-to-atmospheric boundary-layer (ABL) scales, by utilizing both models and long-term measurements collected from the Duke Forest AmeriFlux sites. For the leaf-to-canopy scale, two classical problems motivated by contemporary applications are considered: (1) ‘inverse problem’ – determination of nighttime ecosystem respiration, and (2) forward problem – estimation of two-way interactions between leaves and their microclimate ‘’. An Eulerian inverse approach was developed to separate aboveground respiration from forest floor efflux using mean CO2 concentration and air temperature profiles within the canopy using detailed turbulent transport theories. The forward approach started with the assumption that canopy physiological, drag, and radiative properties are known. The complexity in the turbulent transport model needed for resolving the two-way interactions was then explored. This analysis considered a detailed multi-layer ecophysiological and radiative model embedded in a hierarchy of Eulerian turbulent closure schemes ranging from well-mixed assumption to third order closure schemes with local thermal-stratification within the canopy. For the canopy-to-ABL scale, this study mainly explored problems pertinent to the impact of the ecophysiological controls on the regional environment. First, the possible combinations of water states (soil moisture and atmospheric humidity) that trigger convective rainfall were investigated, and a distinct ‘envelope’ of these combinations emerged from the measurements. Second, an analytical model as a function of atmospheric and ecophysiological properties was proposed to examine how the potential to trigger convective rainfall shifts over different land-covers. The results suggest that pine plantation, whose area is projected to dramatically increase in the Southeastern US (SE), has greater potential to trigger convective rainfall than the other two ecosystems. Finally, the interplay between ecophysiological and radiative attributes on surface temperature, in the context of regional cooling/warming, was investigated for projected land-use changes in the SE region. / Dissertation