AbstractThis study investigated the effect of benthic macrofauna on nutrient fluxes. The influence of the macrofauna on nutrients released from the sediments was investigated experimentally in the laboratory using sediment cores from the Swan–Canning Estuary. Excretion rates of common benthic species were also measured to quantify the role of the macrofauna in estuarine nutrient cycling.The presence of macrofauna increased the release of phosphate and ammonium into the water column but decreased the release, or resulted in uptake, of nitrate by the sediments. There were no significant differences in porewater concentrations of ammonium, nitrate or phosphate between treatments with and without macrofauna. The macrofauna clearly had an important role in nutrient fluxes, as nutrient release differed between cores with and without fauna, and nutrient fluxes were significantly correlated with increased faunal biomass.Other factors, such as season and dissolved oxygen concentrations, influenced the concentration of nutrients released. Ammonium was released into the overlying water column at higher rates in winter than summer, while nitrate was released at higher rates in summer than winter. Aeration did not have a significant effect on nutrient fluxes, however there was a significant increase in filterable reactive phosphorus, and decrease in nitrate, in the porewater of cores which were not aerated.Benthic species excreted phosphate, nitrate and ammonium, with ammonium present in the largest amounts. Comparison of excretion rates to the amount of nutrients released into the water column in the core experiments revealed that excretion could account for 30% of the phosphate and >200% of the ammonium measured in the water column.Clearly the benthic macrofauna have a significant role with respect to benthic nutrient fluxes within the Swan–Canning Estuary, with benthic regeneration of nutrients estimated to equal external loading of nutrients. However, further work is required to more precisely define the influence of seasonality, dissolved oxygen, microbial activity and sediment characteristics on nutrient fluxes. Copyright © 2001 John Wiley & Sons, Ltd.