The determination of ecosystem carbon balances is a major issue in environmental research. Forest inventories and – more recently – Eddy covariance measurements have been set up to guide sustainability assessments as well as carbon accounting. A differentiation between ecosystem compartments of carbon such as soil and vegetation, or above- and belowground storages nevertheless requires further empirical assumptions or model simulations. However, models to estimate carbon balances often do not account for carbon export by management and the direct and indirect impacts of forest management. To overcome this obstacle, we complemented a physiologically based process model (MoBiLE-PSIM) with routines for dimensional tree growth and mortality and evaluated the full model with measurements of water availability, primary production, respiration fluxes and forest development (tree dimensions and numbers per hectare). The model is applied to three forests representing different physiological types and climatic environments: Norway spruce, European beech and Mediterranean holm oak. Simulated carbon balances are presented on a daily, annual and decadal time scale throughout the years 1998–2008 for all three stands. On average, gross primary production is 2.0, 1.7, and 1.4 and net ecosystem production 0.6, 0.6, and 0.3 kg Cm−2 a−1. Export of carbon by thinning is highest in the middle-aged beech stand (0.24 kg Cm−2 a−1) which decreases net ecosystem production by 15% compared with an unthinned stand. Between 46 (spruce) and 72 (oak) % of carbon gained by net ecosystem production is sequestered below ground (incl. roots) – a share that is decreased if a part of the carbon is exported as timber. The role of further impacts, in particular carry-over effects in years that follow intense drought periods, is highlighted and the usefulness of the approach for highly resolved environmental change studies is discussed.