Background: Capturing the response of forest ecosystems to inter-annual climate variability is a great challenge. In this study, we tested the capability of an individual-based forest gap model to display carbon fluxes at yearly and daily time scales. The forest model was applied to a spruce forest to simulate the gross primary production (GPP), respiration and net ecosystem exchange (NEE). We analyzed how the variability in climate affected simulated carbon fluxes at the scale of the forest model. Results: Six years were simulated at a daily time scale and compared to the observed eddy covariance (EC) data. In general, the seasonal cycle of the individual carbon fluxes was correctly described by the forest model. However, the estimated GPP differed from the observed data on the days of extreme climatic conditions. Two new parameterizations were developed: one resulting from a numerical calibration, and the other resulting from a filtering method. We suggest new parameter values and even a new function for the temperature limitation of photosynthesis. Conclusions: The forest model reproduced the observed carbon fluxes of a forest ecosystem quite well. Of the three parameterizations, the calibrated model version performed best. However, the filtering approach showed that calibrated parameter values do not necessarily correctly display the individual functional relations. The concept of simulating forest dynamics at the individual base is a valuable tool for simulating the NEE, GPP and respiration of forest ecosystems.