Understanding the consequences of changes in climatic and biological drivers on tree carbon and water fluxes is essential in forestry. Using a metamodeling approach, sensitivity and uncertainty analyses were carried out for a tree-scale model (MAESPA) to isolate the effects of climate, morphological and physiological traits, and intertree competition on the absorption of photosynthetically active radiation (APAR), gross primary production (GPP), transpiration (TR), light use efficiency (LUE), and water use efficiency (WUE) in clonal Eucalyptus plantations. The metamodel predicting daily TR was validated using one year of sap flow measurements and showed close agreement with the measurements (mean percentage error = 11%, n = 2155). Simulations showed that APAR, GPP, and TR were very sensitive to the tree morphology and to a competition index representing its local environment. LUE and WUE were, in addition, very sensitive to the natural variability of the physiological leaf and root parameters. A maximum percentage error of 10% in these parameters leads to 18%, 17%, 16%, 9%, and 18% uncertainty for APAR, GPP, TR, LUE, and WUE, respectively. The uncertainties in TR were highest for the smallest trees. This study highlighted the need to take account of the spatial and temporal variability of tree traits and environmental conditions for simulations at the tree scale.