Denitrification is a microbial process that takes place on and within sediment and results in the transformation of dissolved inorganic nitrogen to nitrogen gas (N2), which is subsequently lost to the atmosphere. In coastal waters denitrification is an important pathway for the removal of excess nitrogen. Rates of denitrification are typically quantified using either in situ benthic chambers or sediment cores incubated in the laboratory. This study assesses if these two approaches give similar fluxes and denitrification efficiencies. This dataset gives fluxes of: i) dissolved oxygen (DO); ii) nitrogen gas (N2); iii) dissolved inorganic nitrogen (DIN); iv) nitrate (NO3-); v); nitrite (NO2-) and vi) ammonium (NH4+) between the sediment and the water column. Results are obtained using core cylinders incubated in the laboratory and in situ benthic chambers. Fluxes are expressed as µmol m-2 of seafloor surface day-1. Denitrification efficiency is also reported and represents the flux of N2 as a proportion of the total flux of DIN. Studies were carried out in Port Phillip Bay at Clifton Springs and Williamstown, Victoria in March and May 2004, respectively. The flux of oxygen, ammonium, nitrate, nitrite and the denitrification efficiency was found to differ between in situ benthic chambers and laboratory incubated sediment cores. Additional experiments were conducted to assess if the abundance of macrofauna in sediments of core cylinders and benthic chambers differed; and ii) if physical disturbance associated with the collection and transport of core cylinders could account for the observed differences.
