This chapter summarizes the methods, results, and conclusions of a 5-year research project (SoilTrEC: Soil Transformations in European Catchments) on experimentation, process modeling, and computational simulation of soil functions and soil threats across a network of European, Chinese, and United States Critical Zone Observatories (CZOs). The study focused on the soil functions of biomass production, carbon storage, water storage and transmission, water filtration, transformation of nutrients, and maintaining habitat and genetic diversity. The principal results demonstrate that soil functions can be quantified as biophysical flows and transformations of material and energy. The functions can be simulated with mathematical models of soil processes within the soil profile and at the critical zone interfaces with vegetation and atmosphere, surface waters and the below-ground vadose zone and groundwater. A new dynamic model for soil structure development, together with data sets from the CZOs, demonstrate both seasonal fluctuations in soil structure dynamics related to vegetation dynamics and soil carbon inputs, and long-term trends (decadal) in soil carbon storage and soil structure development. Cross-site comparison for 20 soil profiles at seven field sites with variation in soil type, lithology, land cover, land use, and climate demonstrate that sites can be classified, using model parameter values for soil aggregation processes together with climatic conditions and soil physical properties, along a trajectory of soil structure development from incipient soil formation through productive land use to overly intensive land use with soil degradation. A new modeling code, the Integrated Critical Zone model, was applied with parameter sets developed from the CZO site data to simulate the biophysical flows and transformations that quantify multiple soil functions. Process simulations coupled the new model for soil structure dynamics with existing modeling approaches for soil carbon dynamics, nutrient transformations, vegetation dynamics, hydrological flow and transport, and geochemical equilibria and mineral weathering reactions. Successful calibration, testing, and application of the model with data sets from horticulture plot manipulation experiments demonstrate the potential to apply modeling and simulation to the scoping and design of new practices and policy options to enhance soil functions and reduce soil threats worldwide.