The emission of a large amount of anthropogenic carbon dioxide (CO2) changes the global carbon cycle, contributing to temperature increase as well as ocean acidification. In addition, the global nitrogen cycle, which is perturbed by industrial fixation, is thought to affect the global carbon cycle. In this review paper, we first introduce how the natural environment changes owing to CO2 emission and nitrogen fixation. To project future global climate and biogeochemical changes, an Earth system model (ESM) including the global carbon and nitrogen cycles is under development. To embed into the new ESM, we developed a new marine ecosystem model that includes riverine and atmospheric nitrogen inputs as well as iron and phosphate cycles. We briefly introduce this marine ecosystem model. It is well known that the mixing process in the ocean controls the water, carbon, and nitrogen cycles. However, in theparameterization of diapycnal mixing employed in ESMs, the physical processes causing mixing have not been well considered thus far. For further development of an ESM, a new parameterization is required.