Carbon dioxide emissions from Sydney Harbour have been measured for the first time. While a relatively small 1000 tonnes a year – the equivalent of 200 cars on the road a year – the new study shows that managing our harbour's carbon footprint will become more important as Sydney's population grows towards 10 million in 2100.

The lead author of the study, Edwina Tanner from the Sydney Institute of Marine Studies, said urban planners could use the results from her studies to better plan how stormwater and other inputs into the harbour are managed.

A Sydney Water spokesperson said: "Better planning and management of stormwater can only result in improved waterway health."

Overall, the Sydney Harbour system – from the heads to the upper reaches of Middle Harbour, and Parramatta and Lane Cove rivers – is a net emitter of carbon dioxide. However, Ms Tanner found that there were areas that were carbon sinks and other areas – particularly the upper parts of the system – that were carbon emitters.

Ms Tanner, who did her study in collaboration with the Centre for Coastal Biogeochemistry at Southern Cross University, said the upper arms of the Sydney river system "are not well flushed".

"Heat builds up leading to increased bacteria and degradation of the system," she said. This effect is seasonal, peaking in spring.

Seasonal variation in carbon dioxide in the Sydney Harbour system. Photo: Edwina Tanner

Ms Tanner emphasised that Sydney Harbour was overall a healthy system, but said by measuring its carbon emissions now and establishing a baseline will allow us to monitor how it responds to further urban growth.

"The harbour has been cleaned up, it's doing well. There are mangrove systems thriving along the Parramatta River now. The whole system flushes and filters well," she said.

"However, there are hidden problems such as heavy metals, PCBs, organochlorines hidden in the sediments. That's partly why we don't eat fish west of the Harbour Bridge."

Ms Tanner had expected increased carbon emissions after high rainfall events. However the contrary turned out to be the case for the system overall.

"Although emissions were enhanced in the upper sections of the estuary ... the biological stimulated air-water emissions in the mid and lower estuary ... transitioned the [whole system] into a sink drawing down carbon dioxide," the paper said.

This shows a dynamic system, where phytoplankton (sea plants and algae) in the lower estuary act as a "biological pump" consuming the carbon dioxide.

Ms Tanner took more than 3500 measurements throughout the harbour system for her study.

Understanding how carbon cycles through the environment is an important part of managing human-induced climate change. Oceans overall are carbon sinks – and the absorption of carbon dioxide is making oceans more acidic.

Estuaries, however, are net carbon emitters. This is a natural phenomenon, but is also being affected by human activity.

Ms Tanner's study, published on Monday in Estuarine, Coastal and Shelf Science, seeks to understand the process of carbon dioxide emission from a drowned river valley adjacent to an emerging megacity.

The paper cites a recent estimate of total emissions from estuaries at between 100 billion and 250 billion kilograms. While this sounds a lot, it is a small fraction of the world's overall carbon "budget", including human and natural sources.

Estuaries, however, are very high emitters per metre squared compared to other ecosystems, so managing them is crucial, Ms Tanner said.

Ms Tanner, a doctoral candidate at the University of Sydney, said that carbon emissions in Sydney were significantly lower than river systems in Asia and Europe.

"Emissions in Sydney Harbour were lower but similar to other natural drowned river valleys in the USA, including the York River [in Virginia] ... and the Hudson River [in New York]," according to Ms Tanner's paper.

Co-author of the study, Professor Bradley Eyre from SCU, said: "A detailed analysis of emissions from urban harbours worldwide could provide an understanding of adaptation strategies needed to manage and protect estuaries from future development and climate change."

"Monday is World Environment Day," Ms Tanner said. "So it's a good moment to look at how we account for our carbon emissions.

"We seem to be more obsessed with measuring money and not the things that really matter, such as how we look after our environment."

Ms Tanner said the next steps would be through a world harbour project. She hopes her post-doctoral work will take this methodology to 27 world harbours, to ensure our understanding of emissions from urban harbours was "measurable and manageable".

The Herald also sought comment from the NSW Office of Environment and Heritage, Environmental Protection Authority and Greater Sydney Commission.