How eco-physiological, biogeochemical and micrometeorological theory can be used to compute biosphere–atmosphere, trace gas exchange rates is discussed within the framework of a process model. The accuracy of the theory is tested by comparing computations of mass and energy flux densities (water vapor, sensible heat, CO2 and ozone) against eddy covariance measurements over five distinct canopies (wheat, potato and soybean crops and a temperate broad-leaved and a boreal conifer forest). Once tested, the theory is used to evaluate how interactions between climate and vegetation might influence leaf area and photosynthetic capacity and, in turn, alter energy balance partitioning and the transfer rates of CO2 and other trace gases over vegetation canopies. Model parameters, derived from biogeochemical and eco-physiological principles, enabled the model to estimate rates of mass and energy exchange with reasonable fidelity. In particular, the theory reproduced the magnitudes and distinct diurnal patterns associated with mass and energy fluxes over a spectrum of vegetation types. Model sensitivity tests revealed that variations in leaf area index and photosynthetic capacity interacted to increase rates of evaporation and carbon dioxide and pollutant uptake, greatly, and in a curvilinear manner. Finally, we conclude that the assignment of many model parameters according to plant functional type has much potential for use in global and regional scale ecosystem, climate and biogeochemistry models.