Degree Name

Doctor of Philosophy


School of Chemistry


This study outlines the development and application of an automated in situ system capable of monitoring multiple carbon and nitrogen based species at high temporal resolution. This system was utilised in three week long nearshore (water depth < 1 m) field studies at three sites within Lake Illawarra, NSW, Australia during three seasons (Winter 2006, summer 2007 and winter 2007). Hourly gas flux measurements ranged from - 4.0 to 42.4 mmol CO2/m2/h, -1.7 to 3.1 μmol N2O/m2/h and –0.007 to 1.6 mmol CH4/m2/h. Coincident measurements of key aqueous and sediment nitrogenous nutrients (including organic carbon and nitrogen, ammonia and nitrite + nitrate) and environmental parameters (pH, dissolved O2, temperature, photosynthetic active radiation (PAR) and salinity) were also made. Diurnal and seasonal shifts in dissolved oxygen concentrations (0 to 7.5 ppm), pH (6.83 – 8.83), PAR (0 to 2500 mmol/m2/s) and air, water and sediment temperature were observed. Diurnal cycles in CH4 and N2O flux, strongly related to changes in dissolved O2 and temperature, were also apparent at some sites.

Benthic metabolic rates were measured directly by combining the CO2 flux measurements with temperature, salinity and pH measurements in a simple carbonate equilibrium model to determine the change in the inorganic carbon content of the water and indirectly using the change in the dissolved O2 concentration as a proxy for carbon processing. The hourly inorganic carbon-based benthic metabolism data showed periods of dark inorganic carbon fixation when C:N ratios were high. This is the first reported in situ evidence that, under high C:N, non-photosynthetic inorganic carbon uptake can play a large role in primary production. A comparison of the daily mean O2 and inorganic carbon-based benthic metabolism data suggests that in winter this periodic anaerobic organic carbon production was balanced by anaerobic organic carbon consumption and that any net change in the organic carbon content of the sediments was driven by aerobic rather than anaerobic processes.

The sites chosen represented three different sediments types – one rich in organic carbon and nitrogen (4 - 5 times richer than the other two sites), two protected from sediment disturbance and one prone to sediment disturbance. The results from these sites were used to examine the effects of sediment disturbance on, and relate differences in sediment and aqueous nutrient composition to changes in, the carbon and nitrogen cycling pattern of the estuary. Disturbance events were found to lead to short term (within 24 hours) decreases in benthic metabolic rates (respiration, net ecosystem production and primary production), dissolved oxygen (up to 1.2 ppm) and pH (up to 0.2 pH units) and increases in aqueous nitrogen concentrations, turbidity and gaseous fluxes. Sediments prone to these events also tended to have lower overall rates of benthic metabolism (by at least a factor of 2), even during disturbance free periods, most likely due to the detrimental effect of frequent sediment disturbance on the structure and diversity of the benthic community. The data, although limited, showed sediments rich in organic carbon and nitrogen to have benthic metabolic rates at least double those of sites with less organic matter. Sediments with less organic matter acted as annual net N2O sinks (-1.4 and -1.8 mmol/m2/yr for the exposed and protected sites, respectively) while the richer sediments, which were characterised by high NO3- availability, moisture content and fine particle size content, acted as an N2O source (1.4 mmol/m2/yr). Earlier studies which focused on deeper water (water depth > 3 m) areas had only observed annual N2O sources.

The nearshore location of the areas examined in this study mean that not only do they experience larger diurnal and seasonal swings in dissolved oxygen, temperature and pH than deeper water areas but they are also particularly susceptible to external influences (e.g. nitrogenous nutrient inputs) and hence highly sensitive to anthropogenically induced changes. These “edge effects” need to be accounted for in order to assess the human impact on these estuarine systems and the global and regional carbon and nitrogen cycling contributions of these systems.

The importance of nearshore estuarine sites as sources (and sinks) of greenhouse gases was also assessed. Estimates of greenhouse gas flux from estuarine and lagoon systems were small, 0.19 to 26.9 Mt/yr CO2-e (depending on the land area estimate used), but of the order of sources already accounted for under United Nations framework convention on climate change (UNFCCC) reporting protocol. These fluxes suggest that anthropogenically driven estuarine greenhouse gas (GHG) production could account for, depending on land area estimate used, between 0.4 and 60 % of all of Australia’s ‘land use change’ based greenhouse gas production. However, the fraction of this flux that is truly anthropogenically driven is unclear as there are no measurements of pristine Australian ecosystems. As such, they should be further investigated and included in future greenhouse gas budgets.



Unless otherwise indicated, the views expressed in this thesis are those of the author and do not necessarily represent the views of the University of Wollongong.