The biogeochemical cycles of biologically important elements are coupled to each other via the formation of biomass. Many ecosystem models assume this coupling to follow fixed stoichiometric ratios, even though, under certain environmental conditions, the stoichiometric composition of marine phytoplankton can deviate strongly from fixed Redfield ratios. This thesis investigates the effect of variable phytoplankton stoichiometry on large scale biogeochemical fluxes in different marine biological systems. In the first study, an ecosystem model is developed for a shallow coastal tidal basin in the Danish-German Wadden Sea and the adjacent North Sea. The model allows for variations in the cellular quotas of carbon (C), nitrogen (N), and chlorophyll (Chl) of the simulated phytoplankton biomass. The phytoplankton C:N ratio in the tidal basin is found to vary from 5 to 15 between light-limited winter conditions and nitrogen-limited summer growth conditions, respectively. Different water depths between the North Sea and the shallow tidal inlet lead to differences in phytoplankton C:N ratios that can also induce a decoupling of carbon and nitrogen fluxes in the budgeting of the annual tidal transport between the North Sea and the Wadden Sea. The second study extends the parameterization of phytoplankton growth by inclusion of the elements silicon (Si) and iron (Fe) to obtain a parameterization for diatom growth that can be applied in diatom-dominated high-nutrient low-chlorophyll (HNLC) ocean regions like the Southern Ocean. The parameterization considers separate pools of cellular chlorophyll, carbon, nitrogen, and silicon and reproduces the elevated Si:N uptake ratios of diatoms growing under iron-limitation. In the third study, the parameterization of diatom growth is applied to an ecosystem model that is coupled to a global setup of the ocean general circulation model of the Massachussets Institute of Technology (MITgcm). The model is adjusted to the Southern Ocean ecosystem and analysed for the biogeochemical fluxes of silicon and nitrogen in the Southern Ocean. Low iron concentrations in the Antarctic Circumpolar Current (ACC) lead to elevated Si:N uptake ratios of Southern Ocean diatoms and a stronger depletion of dissolved silica over dissolved inorganic nitrogen in northwards flowing surface waters. The northwards flowing surface waters are subducted and involved in the formation of Southern Annular Mode Water (SAMW) which later becomes Antarctic Intermediate Water (AAIW) and supplies the North Atlantic Ocean with nutrients. The stoichiometric signature of SAMW and the supply of nutrients to the North Atlantic thus depends on the decoupling of silicon and nitrogen metabolism in diatoms and its dependence on iron concentrations in Southern Ocean surface waters. The fourth study focuses on scalability and computational costs of a high-resolution model version of the described global biogeochemical model on a multi-processor supercomputer. The models analysed in this thesis present a progression towards the development of a global biogeochemical ocean general circulation model that realistically reproduces nutrient distributions as a basis to make future predictions of global carbon fluxes.