We investigated the relative importance of climatic versus biotic controls on gross primary production (GPP) and water vapor fluxes in seasonally drought-affected ponderosa pine forests. The study was conducted in young (YS), mature (MS), and old stands (OS) over 4 years at the AmeriFlux Metolius sites. Model simulations showed that interannual variation of GPP did not follow the same trends as precipitation, and effects of climatic variation were smallest at the OS (50%), and intermediate at the YS (<20%). In the young, developing stand, interannual variation in leaf area has larger effects on fluxes than climate, although leaf area is a function of climate in that climate can interact with age-related shifts in carbon allocation and affect whole-tree hydraulic conductance. Older forests, with well-established root systems, appear to be better buffered from effects of seasonal drought and interannual climatic variation. Interannual variation of net ecosystem exchange (NEE) was also lowest at the OS, where NEE is controlled more by interannual variation of ecosystem respiration, 70% of which is from soil, than by the variation of GPP, whereas variation in GPP is the primary reason for interannual changes in NEE at the YS and MS. Across spatially heterogeneous landscapes with high frequency of younger stands resulting from natural and anthropogenic disturbances, interannual climatic variation and change in leaf area are likely to result in large interannual variation in GPP and NEE.