Abstract. Biogeochemical models that simulate realistic lower trophic levels dynamics, including the representation of main phytoplankton and zooplankton functional groups, are valuable tools for our understanding of natural and anthropogenic disturbances in marine ecosystems. However, previous three-dimensional biogeochemical modeling studies in the northern and deep Gulf of Mexico (GoM) have used only one phytoplankton and one zooplankton type. To advance our modeling 15 capability of the GoM ecosystem and to investigate the dominant spatial and seasonal patterns phytoplankton biomass, we configured a 14-component biogeochemical model that explicitly represents nanophytoplankton, diatoms, micro-, and mesozooplankton. Our model outputs compare well with satellite and in situ observations, reproducing dominant seasonal patterns in chlorophyll and primary production. The model results show that diatom growth is strongly silica limited (>95%) in the deep GoM, and both nitrogen and silica limited (30-70%) in the northern shelf. Nanophytoplankton growth is weakly 20 nutrient limited in the Mississippi delta year-round (<20%), and strongly nutrient limited in the deep GoM during summer (~80%). Such nutrient limitation patterns influence the spatial and seasonal phytoplankton composition, with the mean diatom to total phytoplankton biomass ratio ranging from ~0.5 near the Mississippi delta to <0.1 in the deep GoM. The examination of primary production and net phytoplankton growth indicates that the biomass losses, mainly due to zooplankton grazing, play an important role modulating the seasonal biomass patterns of the nanophytoplankton and 25 diatoms. Our analysis further shows that the dominant physical process influencing the net phytoplankton growth is horizontal advection in the northern shelf, and vertical diffusion in the deep GoM. This study highlights the importance of representing small and large size plankton dynamics to describe primary production patterns, and emphases the needs for an integrated analysis of biologically and physically driven biomass fluxes to better understand phytoplankton biomass phenologies in the GoM. 30Biogeosciences Discuss., https://doi