A one-dimensional, multilayer model that infers the fluxes of heat, water vapor, and CO2 in a biosphere-atmosphere system, as well as their sources and sinks, was described and evaluated in a secondary broad-leaved forest. Coupling of a third-order closure model allows the model to infer profiles of scalar fluxes, sinks, and sources with the computed velocity statistics. Furthermore, the model combines a leaf water process model and makes it possible to capture the impacts of rainfall events on the fluxes, sinks, and sources. The model test was conducted for the two periods (rain and nonrain events) to investigate whether the proposed model can reproduce the profiles of scalar fluxes, sinks, and sources in different weather conditions in the experimental forest. Modeled scalar and heat fluxes for the nonrainfall period showed generally good agreement with measurements. Model calculation showed that CO2 sink of the canopy during rainfall decreased, since the deep canopy layers work as a source due to least radiation transferred to the deep layers. After rainfall, evaporation from wetted leaves caused low vapor pressure deficit (VPD) between the leaf and air, creating favorable conditions for stomatal conductance and intercellular CO2 concentration, which consequently increases carboxylation rates in the photorespiratory carbon oxidation cycle. These results suggest that photosynthesis rates during and after rainfall events are primarily influenced by radiation as well as a variety of environmental factors, particularly VPD. The model results also indicated that the maximum source/sink strengths of heat and H2O were distributed within the top 30% of the canopy and that the CO2 distribution had the feature of the vegetation shape. These differences imply that the roughness heights of individual components are different, causing different effective exchange heights.