Nutrient dynamics in estuaries are temporally variable in response to changing physical–chemical conditions and biogeochemical processes involving primary producer groups such as phytoplankton, microphytobenthos, seagrass and macroalgae. In order to reveal intra-annual changes in the biomass of primary producer groups and associated changes in estuarine nutrient dynamics, we developed a box model, coupling water inflows and outflows and nitrogen dynamics in Wilson Inlet, a large, central-basin-dominated, intermittently closed estuary exposed to a Mediterranean climate in Western Australia. The model is calibrated and validated with monitoring data, aquatic plant biomass estimates and biogeochemical rate measurements. Macrophytes and their microalgal epiphytes appear to rapidly assimilate nutrients from the first flush from the catchment in winter, but this buffer capacity then ceases, and a phytoplankton ‘bloom’ develops in response to subsequent river runoff events in spring. Significant amounts of bioavailable nitrogen are exported to the ocean because phytoplankton predominance occurs while the sand bar is breached. Surface sediments play a key role for nitrogen dynamics: In late spring to autumn, high light availability at the sediment surface stimulates high primary production by microphytobenthos, leading to reduced benthic ammonium fluxes particularly in the deep basin. Microphytobenthos contributes about 60% of annual whole-system primary production. Despite high benthic primary production, nitrogen release from sediments is the biggest nitrogen source to the estuary.
