From south-bound cane toads, invasive weeds and fluctuating fish stocks, new research has revealed what's in our waterways and how they are influenced by natural disasters.
The major study of NSW estuaries, led by Southern Cross University and funded through the Riparian Stabilisation Package of the NSW Estuary Asset Protection (NEAP) Program, has created the first biodiversity map of major river mouths and coastal tributaries along a 1,000 kilometre stretch of coastline, using a novel technique called eDNA.
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So we've been working on creating a new biodiversity baseline for the estuaries in New South Wales. So the project is a part of the New South Wales Estuary Asset Protection Program, which was created in response to the floods of 2022. What we noticed is we just don't understand how bad the influence was on our estuaries and what lives in the estuaries.
So what we're trying to do is create a new baseline to understand what lives in the estuaries from the smallest microbe to the biggest fish, to mammals that live in the estuaries, to know that in the future, if there's other disasters, say floods, bush fires, so we can understand what changed and how we can manage the effects of those, of those impacts.
One of the biggest methods we use is something called eDNA, metabarcoding. EDNA stands for. Environmental, DNA is something that's everywhere in the environment. Um, it relies on traces of DNA, that living species sheds. So it's everything from humans to fish to trees, algae, everything sheds, DNA in the environment.
And what we do is we use a method that's very similar to detecting COVID in the wastewater to detect all of these species. In the past year we've gone to almost 300 sites. They go from the very north of New South Wales, down to the south, close to the border of Victoria.
Our biggest collaborator is the New South Wales Department of Primary Industries and Regional Development. And so we work very closely with them to do these surveys. We also work very closely with different Indigenous groups across the state. So at the moment we work with six different mobs.
It's quite a nice way to co-create knowledge and, and co-design where we are going.
So the way we collect the samples is we take a few buckets of water, we go to the creek or to the estuary, and we just scoop up a couple of litres of water. The next step is that we filter that water through a small filter and that filter goes off to the lab where they then extract the DNA and then study what's actually where the DNA comes from.
The powerful thing that I still think is, is quite amazing that from just the bucket of water and a tiny little filter, we can detect thousands and thousands of species.
At the moment in our dataset, we've got almost 10,000 taxa. So that's, that's a lot of species. A lot of those are bacteria, little microbes that we can use and we can use to study, for example, nutrient cycling after big floods. But all of them are also bigger animals that we are of interest to fishes, like we've detecting mulloway, we're detecting bream, even detecting sharks.
What we're already seeing is quite a strong effect of the recent floods caused by ex-tropical cyclone Alfred.
We went to the Northern Rivers area, we resurveyed. A lot of the sites that we had, and what we can see is that the species that live in the estuaries, they really shift with these floods. And so one of the plans for next year is to look at whether the rivers recover quickly and which. Estuaries recover quicker than others.
Ultimately, all of that data will be of use, so we can protect our environment and we can manage it better in a way that we can use estuaries in a sustainable way into the future.
Environmental DNA, or eDNA, is similar to the technology employed to detect COVID fragments in wastewater during the COVID-19 pandemic. This highly sensitive technology is being increasingly used around the world to identify the origins of organic material, from algae blooms in lakes to critically endangered species in the ocean.
It relies on discarded genetic material in the environment, such as scales, faeces, fur or skin.
Southern Cross researchers, in collaboration with colleagues from the NSW Department of Primary Industries and Regional Development (DPIRD) and with assistance from local Indigenous ranger networks, collected samples from 34 estuaries along the NSW coastline on 234 separate sites, in both summer and winter.
They used a particular technique known as eDNA metabarcoding. This technique samples for many species at the same time, by extracting DNA from water or sediment. The short DNA sequences extracted (barcodes) are then mapped to reference databases.
Lead investigator Dr Maarten De Brauwer of Southern Cross University said the data paints a fascinating picture of the species living in and around NSW coastal tributaries, including birds, worms, plants, fish, sharks and invasive pests.
"The data revealed the location of 68 invasive pest species in various rivers, including aquatic weeds, algae and even cane toads further south than previously thought."
Dr De Brauwer said the project, part of the NEAP program developed after the 2022 floods, provided much-needed baseline data for managing critical ecosystems.
"This data can show what is actually happening to our biodiversity in estuaries following disasters like floods and bushfires. This can inform management agencies, biosecurity responses and help the ranger network manage these complex and dynamic systems after major disasters to support species recovery," he said.
This baseline is already being put to the test. Dr De Brauwer's team recently returned to sample sites following Tropical Cyclone Alfred and the extreme rain events of March 2025 to compare data.
This will be a valuable addition to the current mapping which includes more than 7,000 species. This data is available as an interactive map on the public site of the lab that completed the DNA analysis, Wilderlab: https://wilderlab.co/explore
Some of the sample sites produced surprising results.
"While the collection method is simple, the technology is incredibly sensitive and some of our results required some sleuthing," said Dr de Brauwer.
"For example, we found water buffalo DNA in the Richmond River, very far from where you would expect to find it. When we went to look for the source, we found a horse trainer along the river was using four water buffaloes named Bob, Ben, Bill and Bruce to train horses, which explained it!"
Where water quality is poor, for example in post-flood or post-cyclone conditions, the technique can offer a quick and cheap solution.
DPIRD Fisheries Technician Kait Harris said estuaries – the middle ground between the ocean and rivers – do not have recent state-wide biodiversity baselines.
"This data is very valuable to understand how we manage them, particularly in challenging circumstances like natural disasters.
"When we are sampling, people are really interested in what we are doing. Fishers, boaties and everyone in the community use estuaries for recreational fishing, swimming, or even work. It's a very visible ecosystem that can be heavily impacted by natural disasters," she said.
Indigenous ranger groups have been important partners in the project said Dr De Brauwer, helping to collect samples and also contributing local knowledge about the sample sites.
The Riparian Stabilisation Package of the NSW Estuary Asset Protection Program is jointly funded by the Australian Government and NSW Government under the Disaster Recovery Funding Arrangements.
