The individual-based EFIMOD simulation model was used for regional-scale assessments of the dynamics of basic characteristics of the carbon and nitrogen balance in the forest ecosystems of north central Russia. Two forest strict nature reserves were chosen as case studies. Data from the National Forest Inventory were used for model initialization. Initial soil data were taken from a soil survey database containing data on soil organic matter and nitrogen content in the organic layer and mineral soil for different forest types and regions of European Russia. Standard meteorological data were used as climatic inputs. Two simulation scenarios (without disturbances and with forest fires) were coupled with 2 climatic ones (actual climate and the scenario of climate change). The main sources of uncertainty were analyzed and the model parameters were evaluated. A Monte Carlo procedure was applied for evaluation of the robustness of coefficients. Simulation results showed that the greatest carbon accumulation occurred in the scenario without disturbances. Fires resulted in significant losses in soil organic matter and tree biomass through direct and indirect carbon dioxide emissions. Simulated climate change led to an increased decomposition rate of soil organic matter and a related increase in the productivity of vegetation; however, for this region, the carbon balance was positive. This was primarily because young and middle-aged stands are prevalent in the region modeled. A full analysis would require analytical data on the possible dynamics of mature and over-mature forests in the same scenarios of climate change and forest fires.