The ability to accurately predict land-atmosphere exchange of mass, energy, and momentum over the coming century requires the consideration of plant biochemical, ecophysiological, and structural acclimation to modifications of the ambient environment. Amongst the most important environmental changes experienced by terrestrial vegetation over the last century has been the increase in ambient carbon dioxide (CO2) concentrations, with a projected doubling in CO2 from preindustrial levels by the middle of this century. This change in atmospheric composition has been demonstrated to significantly alter a variety of leaf and plant properties across a range of species, with the potential to modify land-atmosphere interactions and their associated feedbacks. Free Air Carbon Enrichment (FACE) technology has provided significant insight into the functioning of vegetation in natural conditions under elevated CO2, but remains limited in its ability to quantify the exchange of CO2, water vapor, and energy at the canopy scale. This paper addresses the roles of ecophysiological, biochemical, and structural plant acclimation on canopy-scale exchange of CO2, water vapor, and energy through the application of a multilayer canopy-root-soil model (MLCan) capable of resolving changes induced by elevated CO2 through the canopy and soil systems. Previous validation of MLCan flux estimates were made for soybean and maize in the companion paper using a record of six growing seasons of eddy covariance data from the Bondville Ameriflux site. Observations of leaf-level photosynthesis, stomatal conductance, and surface temperature collected at the SoyFACE experimental facility in central Illinois provide a basis for examining the ability of MLCan to capture vegetation responses to an enriched CO2 environment. Simulations of control (370 [ppm]) and elevated (550 [ppm]) CO2 environments allow for an examination of the vertical variation and canopy-scale responses of vegetation states and fluxes to elevated CO2. The unique metabolic pathways of the C3 soybean and C4 maize produce contrasting modes of response to elevated CO2 for each crop. To examine the relative roles of direct reduction in stomatal aperature, observed structural augmentation of leaf area, and biochemical down-regulation of Rubisco carboxylation capacity in soybean, a set of simulations were conducted in which one or more of these acclimations are synthetically removed. A 10% increase in canopy leaf area is shown to offset the ecophysiologically driven reduction in latent energy flux by 40% on average at midday. Considering all observed acclimations for soybean, average midday LE (H) were decreased (increased) by 10.5 (18) [W m−2]. A lack of direct stimulation of photosynthesis for maize, and no observed structural or biochemical acclimation resulted in decreases (increases) in average midday LE (H) by 40–50 [W m−2]. An examination of canopy-scale responses at a range of CO2 concentrations projected to be seen over the coming century showed a general continuation in the direction of flux responses. Flux responses showed little sensitivity to assumptions of constant versus linear trends in structural and biochemical acclimation magnitudes over the 400–700 [ppm] concentration range examined here.