Carbon gain from gross primary production is the single largest term in the terrestrial carbon budget, but the carbon balance is controlled not just by photosynthesis. Allocation of carbon to the growth of leaves, wood, and roots, loss of carbon during autotrophic respiration, and carbon turnover (comprising litterfall, background mortality, and disturbances) are critical determinants of carbon storage. Litter decomposition and resulting soil organic matter formation provide a long-term carbon store. Associated with the flows of carbon through an ecosystem is the parallel flow of nitrogen and other nutrients. This chapter develops the ecological foundation and mathematics to describe ecosystem carbon dynamics using biogeochemical models. The CASA-CNP model is used to illustrate the basic details of biogeochemical models