Diatoms are important primary producers within pelagic, benthic, and epiphytic communities, and their siliceous frustules sink rapidly to the sediment. We measured benthic nutrient and gas fluxes and water column and sediment properties in an estuary of southeastern Australia to identify control mechanisms coupling benthic and pelagic processes, in particular, how nutrients become fractionated by processes affecting benthic nutrient fluxes. During late spring, the water column of St. Georges Basin was oligotrophic, primary production was likely phosphorus (P) limited, and the phytoplankton community was dominated by cyanophytes. Molar ratios of dissolved inorganic carbon (TCO 2 ) to silica (Si) benthic fluxes, however, were equal to the molar composition of diatoms, indicating that diatoms preferentially sink and deliver the most labile organic matter fraction to the sediment. The congruent release of Si and carbon (C) implies a coupling of processes mobilizing Si and C. Extracellular polymeric substances surrounding the siliceous frustule are the primary labile organic matter fraction, and their rate of mineralization limits the dissolution of the siliceous frustule. Because decomposing biomass in sediments leads to net di-nitrogen (N 2 ) production and very efficient burial of P, the fate of diatoms significantly contributes to the removal of bioavailable nutrients. High dissolved inorganic nitrogen to dissolved inorganic P benthic flux ratios of 290 to 900 promote P limitation, particularly in shallow waterbodies with long water residence times.