Life cycle analysis of climate and disturbance effects on forest net ecosystem productivity (NEP) is necessary to assess changes in forest carbon (C) stocks under current or future climates. Ecosystem models used in such assessments need to undergo well-constrained tests of their hypotheses for climate and disturbance effects on the processes that determine CO2 exchange between forests and the atmosphere. We tested the ability of the model ecosys to simulate diurnal changes in CO2 fluxes under changing air temperatures (Ta) and soil water contents during forest regeneration with eddy covariance measurements over boreal jack pine (Pinus banksiana) stands along a postclearcut chronosequence. Model hypotheses for hydraulic and nutrient constraints on CO2 fixation allowed ecosys to simulate the recovery of C cycling during the transition of boreal jack pine stands from C sources following clearcutting (NEP from −150 to −200 g C m−2 yr−1) to C sinks at maturity (NEP from 20 to 80 g C m−2 yr−1) with large interannual variability. Over a 126-year logging cycle, annualized NEP, C harvest, and net biome productivity (NBP=NEP–harvest removals) of boreal jack pine averaged 47, 33 and 14 g C m−2 yr−1. Under an IPCC SRES climate change scenario, rising Ta exacerbated hydraulic constraints that adversely affected NEP of boreal jack pine after 75 years. These adverse effects were avoided in the model by replacing the boreal jack pine ecotype with one adapted to warmer Ta. This replacement raised annualized NEP, C harvest, and NBP to 81, 56 and 25 g C m−2 yr−1 during a 126-year logging cycle under the same climate change scenario.