A global three-dimensional marine ecosystem model with several key phytoplankton functional groups, multiple limiting nutrients, explicit iron cycling, and a mineral ballast/organic matter parameterization is run within a global ocean circulation model. The coupled biogeochemistry/ecosystem/circulation (BEC) model reproduces known basin-scale patterns of primary and export production, biogenic silica production, calcification, chlorophyll, macronutrient and dissolved iron concentrations. The model captures observed high nitrate, low chlorophyll (HNLC) conditions in the Southern Ocean, subarctic and equatorial Pacific. Spatial distributions of nitrogen fixation are in general agreement with field data, with total N-fixation of 55 Tg N. Diazotrophs directly account for a small fraction of primary production (0.5%) but indirectly support 10% of primary production and 8% of sinking particulate organic carbon (POC) export. Diatoms disproportionately contribute to export of POC out of surface waters, but CaCO3 from the coccolithophores is the key driver of POC flux to the deep ocean in the model. An iron source from shallow ocean sediments is found critical in preventing iron limitation in shelf regions, most notably in the Arctic Ocean, but has a relatively localized impact. In contrast, global-scale primary production, export production, and nitrogen fixation are all sensitive to variations in atmospheric mineral dust inputs. The residence time for dissolved iron in the upper ocean is estimated to be a few years to a decade. Most of the iron utilized by phytoplankton is from subsurface sources supplied by mixing, entrainment, and ocean circulation. However, owing to the short residence time of iron in the upper ocean, this subsurface iron pool is critically dependent on continual replenishment from atmospheric dust deposition and, to a lesser extent, lateral transport from shelf regions.