The use of environmental DNA (eDNA) – genetic material shed by organisms into their water sediment or soil – is transforming how environmental managers monitor biodiversity and ecosystem health in coastal waterways. eDNA offers a powerful, non-invasive tool to detect species presence, track ecosystem changes, and support conservation efforts in estuaries, mangroves, seagrass beds, and beyond. As a coastal manager in Australia, understanding and utilising eDNA can significantly enhance local environmental monitoring efforts.

Sources of eDNA include a range of animal tissue, including skin cells, mucus, faeces, gametes, and decomposing tissue.

eDNA can be collected and analysed without the need to observe or capture the organisms themselves. This non-invasive monitoring method is particularly useful in monitoring the presence of organisms that are hard to detect visually including rare, cryptic, elusive, migratory and microscopic species making eDNA a powerful tool for biodiversity assessments.

eDNA is less effective in detecting highly mobile species, species with low DNA shedding rates, and species without reference sequences in databases.

eDNA can be used to monitor the biodiversity of communities in a variety of coastal environments such as estuaries, mangrove communities, seagrass beds, and intertidal zones where the detection of changes in species composition over time may be used to identify early signs of ecosystem stress or pollution.

Increasingly, eDNA is increasingly being incorporate into monitoring in management frameworks, with a growing body of guidance supporting its consistent and effective use. The examples in Box 1 highlight the expanding role and application of eDNA in different environments across different state jurisdictions..

While eDNA excels at detecting species presence, currently it cannot be used to accurately estimate abundance or biomass.

Techniques such as quantitative Polymerase Chain Reaction (qPCR) and digital droplet PCR (ddPCR) can provide semi-quantitative data, but eDNA does not provide information on organism health, age, or size.

Consequently, using eDNA to monitor the presence of species should not replace all traditional monitoring methods, especially for visual confirmation or behavioural studies. Combining eDNA with other methods, such as Baited Remote Underwater Video (BRUVs), can provide a more complete picture of biodiversity. BRUVs are good for observing larger, mobile, and visible species, while eDNA excels at detecting small, cryptic, or rare species and microbial diversity.

Use of eDNA in monitoring offers several benefits. It is a non-invasive method, meaning it does not require capturing or directly observing organisms, which reduces stress on wildlife and habitat disturbance. It is also cost-effective, especially when scaled up for large monitoring programs. eDNA is highly sensitive, capable of detecting species at low abundance, and it works well in challenging environments such as remote locations or turbid waters where traditional survey methods may be limited. Additionally, there is significant potential for standardising and automating eDNA workflows, making it a promising tool for consistent and scalable biodiversity monitoring. Plus, with a little training, samples can be collected by citizen scientists, giving more options for widespread sampling.

However, eDNA also has some limitations. Its effectiveness depends on the availability and quality of reference genetic databases to accurately identify species. There is a risk of false positives (detecting species that aren’t actually present) or false negatives (failing to detect species that are present), especially if contamination is not carefully controlled throughout the sampling and analysis process. Interpreting eDNA results can also be complex and often requires expert knowledge to account for environmental factors and biological processes that affect DNA persistence and transport.

Check if there is a guide for your local area e.g. state guidance, or a guide developed by the local research organisation that undertakes eDNA work (e.g., Jame Cook University, Griffith University or University of Queensland, Australian Institute of Marine Science or eDNA Frontier).

Note that although you are likely to require specialised expertise to undertake eDNA monitoring, it is useful to have a general understanding of the steps involved to scope how use of eDNA will fit your broader monitoring objectives (Box 2).