We compared carbon storage and fluxes in young and old ponderosa pine stands in Oregon, including plant and soil storage, net primary productivity, respiration fluxes, eddy flux estimates of net ecosystem exchange (NEE), and Biome-BGC simulations of fluxes. The young forest (Y site) was previously an old-growth ponderosa pine forest that had been clearcut in 1978, and the old forest (O site), which has never been logged, consists of two primary age classes (50 and 250 years old). Total ecosystem carbon content (vegetation, detritus and soil) of the O forest was about twice that of the Y site (21 vs. 10 kg C m−2ground), and significantly more of the total is stored in living vegetation at the O site (61% vs. 15%). Ecosystem respiration (Re) was higher at the O site (1014 vs. 835 g C m−2 year−1), and it was largely from soils at both sites (77% of Re). The biological data show that above-ground net primary productivity (ANPP), NPP and net ecosystem production (NEP) were greater at the O site than the Y site. Monte Carlo estimates of NEP show that the young site is a source of CO2 to the atmosphere, and is significantly lower than NEP(O) by c. 100 g C m−2 year−1. Eddy covariance measurements also show that the O site was a stronger sink for CO2 than the Y site. Across a 15-km swath in the region, ANPP ranged from 76 g C m−2 year−1 at the Y site to 236 g C m−2 year−1 (overall mean 158 ± 14 g C m−2 year−1). The lowest ANPP values were for the youngest and oldest stands, but there was a large range of ANPP for mature stands. Carbon, water and nitrogen cycle simulations with the Biome-BGC model suggest that disturbance type and frequency, time since disturbance, age-dependent changes in below-ground allocation, and increasing atmospheric concentration of CO2 all exert significant control on the net ecosystem exchange of carbon at the two sites. Model estimates of major carbon flux components agree with budget-based observations to within ± 20%, with larger differences for NEP and for several storage terms. Simulations showed the period of regrowth required to replace carbon lost during and after a stand-replacing fire (O) or a clearcut (Y) to be between 50 and 100 years. In both cases, simulations showed a shift from net carbon source to net sink (on an annual basis) 10–20 years after disturbance. These results suggest that the net ecosystem production of young stands may be low because heterotrophic respiration, particularly from soils, is higher than the NPP of the regrowth. The amount of carbon stored in long-term pools (biomass and soils) in addition to short-term fluxes has important implications for management of forests in the Pacific North-west for carbon sequestration.