The General Ensemble Biogeochemical Modeling System (GEMS) enables spatially explicit simulation of carbon dynamics in vegetation and soils. GEMS is a modeling system that was developed for a better integration of well-established ecosystem biogeochemical models with various spatial databases for the simulations of biogeochemical cycles over large areas. It uses a Monte-Carlo-based ensemble approach to incorporate the variability (as measured by variances and covariance) of state and driving variables of the underlying biogeochemical models into simulations. Consequently, GEMS can simulate not only the spatial and temporal trends of carbon dynamics, such as CO₂ exchange between the terrestrial biosphere and the atmosphere, but also can provide uncertainty estimates of the predicted variables in time and space.