Chemical fluxes from the ocean's surface into the deep sea vary over the ocean in response to the supply of nutri- ents, the availability of light and the dispersion of newly-produced material by local turbulence and sinking. This study will lead to the construction of global scale models, which will integrate biological and chemical com- ponents into multi-dimensional ocean circulation models. Already developed are a series of component models describing the upper ocean ecology, water column transformations, and sediment diagenesis, which can be used in circulation models of variable complexity. Two key aspects of upper ocean biology that cause chemical fluxes in the ocean to diverge from the simplest flux concentrations will be emphasized. The first is the presence of unutilized nutrients in high latitude surface water. A hypothetical upper ocean ecosystem model based on size-classes of phytoplankton will be used to account for the notable differences in nutrient utilization observed between oceans. The second aspect is the production of refactory dissolved organic compounds by marine organisms. Results from earlier three-dimensional model studies show that the regeneration of nutrients from sinking particles takes place too high in the water column to account for observed distributions of nutrients and fluxes in the ocean. Advective and diffusive fluxes of refractory dissolved organic compounds appear to be the missing ingredients needed to account for the removal of organic carbon and nutrients from the upper ocean to the deep sea. Models such as these, when verified by field data from other investigators, will permit understanding and prediction of global fluxes of elements such as carbon and nitrogen.