Seasonal variations in major ions, nutrients and chlorophyll a were examined at two sites in the upper reaches of the Swan River estuary, Western Australia. Intra-annual variations between the variables were strongly influenced by seasonal riverine discharge, though major ions behaved highly conservatively across a wide range of salinity. Reduced discharge following winter produced strong density stratification that coincided with upstream salt wedge propagation and produced distinct physico-chemical identities of surface and bottom waters. Anoxia of bottom waters associated with the salt wedge region induced increased concentrations of ammonium and phosphate, especially at the deeper of the two sites. Locally variable groundwater flow may have also been important in transporting sediment porewater nutrients into the water column. The seasonality of riverine discharge produced large intra-annual variations in temperature (13–29°C) and salinity (3–30). Transient increases in turbidity occurred when the salt wedge coincided with the position of sampling locations. The subsequent flocculation process likely contributed to further oxygen consumption and nutrient regeneration from the bottom sediments, while simultaneously depositing nutrient-rich flocs with low molar N:P ratios (3–8) to the sediment surface. Nutrient ratios and absolute nutrient concentrations suggest that nitrogen is the nutrient most likely to limit phytoplankton growth over most of the year.