Survey whole systems by filtering water and sending the filter to us for analysis. Our user-friendly kits contain everything you need to sample eDNA from ponds, lakes, streams, rivers, canals, estuaries, and oceans.

Animals leave traces of DNA in water from shed skin cells, mucous, saliva, urine, faeces and other bodily processes. This ‘environmental DNA’ remains in the water and detectable for a few days and can be captured by filtering the water with our custom-designed eDNA sampling kits. The filter is then sent to our laboratory for analysis according to the services you have selected.

Aquatic eDNA is fast becoming an established tool for monitoring fish, amphibians and other wildlife, and NatureMetrics has been at the forefront of this for the last four years.

Aquatic eDNA Survey

Our recent work with collaborators across Europe through the DNAqua-net project has led to the drafting and submission of the first European standard for eDNA sampling. You can benefit from our global expertise and assistance in applying our sciences and methods across different aquatic systems around the world.

The type of aquatic eDNA analyses you require will depend on the question(s) you are trying to answer, and our team can advise you on what suits your project needs. You may want to ask “which species (multiple) are present in my sample?”. For this, you’d use a multi-species metabarcoding analysis. If you’re asking “is species X (a single species) present in my sample?”, you’ll likely benefit from one of our single-species analyses using qPCR.

Surveying a whole taxonomic group

eDNA Metabarcoding (MBC) uses high throughput sequencing on community DNA to detect and identify diverse taxa in a single reaction.


NatureMetrics Fish MBC Survey service uses metabarcoding of the 12S gene to characterise the fish species diversity in an eDNA sample. We use a custom bioinformatics pipeline coupled with a curated reference database of fish sequences to return high confidence detections. Please note, the species we can identify depends on the completeness of reference databases. Where a species does not match to a sequence in the reference database, it will be assigned taxonomy at a higher level (e.g. family or genus).

Our Vertebrate MBC service targets entire vertebrate communities, including fish, amphibians, mammals and birds. The trade-off of the wider taxonomic breadth is that there are a small number of closely-related pairs of fish species that cannot be separated using this assay. Our team can work with you to decide which is the best assay for the needs of your project.

Our Crayfish MBC Service can simultaneously detect and identify all crayfish species present in Europe, including both the protected white-clawed crayfish (Austropotamobius pallipes, WCC) and invasive species such as the American signal crayfish (Pacifastacus leniusculus). The assay was designed to target all species known to occur in the UK but will also detect many species that occur elsewhere in the world.

Our Amphibian MBC service targets toads, frogs and newts, including both invasive species and protected ones. We have used this assay to detect most of the British native species and have also used it to detect and identify amphibian species from across the world. For example our assay can easily differentiate between the three native UK newt species.

Our Mammal MBC service provides data on aquatic and semi-aquatic animals (including otters, water vole and dolphins where applicable), as well as the terrestrial species that visit the water or whose DNA has been washed into the water by rainfall. Research has shown that eDNA metabarcoding for mammals is at least as powerful as other survey techniques for terrestrial species, providing data on both large (e.g. deer, badgers) and small (e.g. mice, shrews, voles) mammals.

Our Unionidae MBC service targets freshwater mussels from the Unionidae family, including the endangered freshwater pearl mussel (Margaritifera margaritifera), the duck mussel (Anodonta anatina), swan mussel (Anodonta cygnea), depressed mussel (Pseudanodonta complanata) and painted mussel (Unio pictorum).

Our Venerida MBC service targets mussels from other families. This provides good data on the Dreissenidae species such as zebra mussels (Driessena polymorpha) and quagga mussels (Dreissena bugensis), which are invasive in the UK, as well as Sphaeridae species including pea mussels (Pisidium tenuilineatum). It also detects the invasive Asian clam (Corbicula fluminea) and several other clam species.

Our Macroinvertebrate MBC service can capture the DNA of macroinvertebrates in your waterbody. By using eDNA samples instead of conventional invertebrate sampling methods, this service can overcome some of the common challenges when surveying invertebrates in waterbodies, from sample collection and storage to taxonomic limitations.

Our macroinvertebrate MBC service was designed to target freshwater macroinvertebrate groups, and particularly insects. We’ve generated data that detects Chironomid flies, water beetles and some important European Protected Species such as Ephemeroptera (mayflies), Plecoptera (stoneflies), and Trichoptera (caddisflies). These taxonomic groups are captured from the DNA that these aquatic invertebrates leave behind in the environment, so you won’t require taxonomic experts in the field and the samples can be collected and stored at room temperature before sending.

We understand that you may also like to survey invertebrates using bulk samples, and you can visit our invertebrates page to learn more about our bulk invertebrate services.

Confirming the presence of a single species in a water sample

Our qPCR analyses can be used to detect particular species by targeting regions of their genome that are unique to them. 

Signal Crayfish
Great Crested Newts
Crayfish Plague
Zebra Mussels
Chytrid Fungus

Our well-validated qPCR test detects the presence of signal crayfish (Pacifastacus leniusculus). We’ve helped our clients identify signal crayfish in streams, rivers and lakes.

We can also combine this test with a test for the presence of crayfish plague.

We offer a high-quality and high-capacity service for detecting Great Crested Newts (Triturus cristatus) with eDNA. Visit our GCN eDNA page to learn more about our 100 % proficiency rated GCN service.

With four of the introduced crayfish species in the UK known to carry crayfish plague (CP) Aphanomyces astaci, our qPCR CP test will detect the presence of CP in your sample.

We can run a highly sensitive qPCR test to detect the presence of zebra mussels (Dreissena polymorpha), even at low population levels.

The spread of Chytrid Fungus remains a risk during mitigation or conservation activities. NatureMetrics are proud to help wildlife conservationists overcome these issues by testing for Emerging Infectious Diseases. We currently provide tests for both B. dendrobatidis and B. salamandrivorans.

Why NatureMetrics?

The latest in innovative aquatic DNA-based methods yielding high accuracy results.

The NatureMetrics FieldMate App which empowers you to collect and submit your field data on the go.

Leveraging the collective expertise of our highly specialised team, including that of our 12+ postdoctoral level scientists.

Robust quality control procedures at every stage of the process.

A partner that is setting the EU standard for eDNA monitoring. Find out more about our collaborations and projects in the Info Hub.

A quality service – Our kits are tried and tested by diverse groups across the world.

The knowledge your eDNA testing is compliant with all Natural England, UK and EU eDNA requirements, laws and legislations.

NatureMetrics: The Science in Action

Using a collection of our eDNA from Water services, we were able to help our client WWF Peru detect nearly 400 vertebrate species in just 44 water samples from the Peruvian Amazon.
Inside NatureMetrics: Hear from our client WWF Peru.
Our team of researchers was able to collect 44 water samples from 11 sample points along and near the Marañon in only 7 days.” … “The four commercially important fish species were all detected in multiple locations, the number dependent on the species. Moreover, the same samples and analysis detected a total of 392 unique vertebrate taxa, including 273 fish.“… “With NatureMetrics’ innovative aquatic eDNA service, we at WWF Peru were able to fully achieve our survey goal of detecting the spatial distributions of six culturally and commercially important aquatic species along the Marañon river, and we exceeded our goal by also detecting hundreds of additional vertebrate species, which we can now start to take into account in designing a sensitive index of basin-ecosystem health.

Aquatic DNA Survey FAQs

Hex-process DNA icon
What is Environmental DNA (eDNA?)

Environmental DNA or eDNA refers to the nuclear or mitochondrial DNA that an organism releases into the environment. This eDNA can be present wherever an organism has interacted with its environment such as in water, soil, sediments and air. You can collect eDNA samples, send them to us, we will analyse them and inform you of the biodiversity present.

Hex-process DNA icon
When is eDNA sampling useful?

Often environmental DNA (eDNA) tests are necessary for development projects that may impact protected species, particularly, if there are bodies of water within 500 meters of the site. There are several species native to the UK, and protected under The Wildlife and Countryside Act 1981, Great Crested Newts, White Clawed Crayfish, Mussels, and many more, that can be detected by completing an eDNA survey.

Hex-process DNA icon
Is an eDNA survey suitable for me?

If your site has any of the attributes listed in the previous question, then yes, you’ll benefit from an eDNA survey.

Our eDNA kits can help you detect, survey and monitor the biodiversity on your site.

Hex-process DNA icon
Can I use eDNA from water to detect GCN?

The Great Crested Newt is the UK’s most heavily protected amphibian species. Great Crested Newt (GCN) eDNA sampling is a Natural England regulated process involving the collection of a filtered water sample taken at the chosen site, and applying sequencing amplification to detect or deny GCN populations at the site. We offer a 100% proficiency rated GCN eDNA service.

  • eDNA from Water
  • Great Crested Newts
  • Invertebrates
  • Species from Faeces
  • Citizen Science
  • Consultation & Support
  • Training

eDNA from Water / Aquatic eDNA Surveys

Perform fast, powerful, robust surveys of aquatic life with the NatureMetrics’ eDNA from Water services. Our easy-to-use and custom designed sampling kits make the cutting-edge of DNA-based aquatic biomonitoring easily accessible to any user. Since 2016, they have been used to generate high-quality data from ponds, lakes, rivers and oceans, from the equator to the poles.

Great Crested Newts

Test for the presence of Great Crested Newts (GCN) in water using NatureMetrics’ GCN eDNA sampling kits, a service that we have been offering with a strong track-record since 2015.

Great Crested Newts are a European Protected Species so surveys are often a legal requirement. NatureMetrics offers one of the most established and trusted GCN eDNA services, and our team has processed thousands of samples for a variety of clients. We’re proud to score 100% in the 2020 proficiency test – the third year in a row that we have achieved this score.


The NatureMetrics’ Invertebrate services overcome the classic challenges associated with the taxonomic identification of terrestrial and aquatic invertebrates.

We use DNA-based methods to obtain species-level data across all major taxonomic groups of invertebrate bulk samples collected using standard capture methods. These statistically powerful datasets can provide the evidence needed for demonstrating the effects of environmental or management changes on biodiversity.

Species from Faeces

From a faecal sample, it is possible to disentangle complex details about biodiversity. The NatureMetrics’ Species from Faeces services allow for species identification of the ‘doer of the deed’ as well as an assessment of the prey species that were consumed.

Citizen Science

The eDNA Discovery Lab brings biodiversity monitoring into the hands of everybody, whether you are hoping to engage stakeholders in fieldwork, or are curious about your own local biodiversity. We can help you to reveal the life within ponds, rivers, lakes and oceans. We work with local communities, schools, NGOs, and international charities to empower everybody with the tools needed for global change.

Find out more about incorporating Citizen Science into your environmental monitoring or see how you can get involved yourself.

Environmental Policy Consultation & Tender Support

NatureMetrics have assisted clients from a variety of sectors in utilising DNA-based methods to meet environmental monitoring needs across a range of regulatory environments.

Our team of experts can help you recognise the relationship between your business and biodiversity and buy-in from regulators and policy-makers, involving them in pilot studies and field trials at early stages. We are highly experienced at bringing together multi-stakeholder groups to trial and demonstrate new technologies and help accelerate uptake.

You can also leverage the knowledge of our team in tender support for environmental projects. We can help you understand how DNA based monitoring can support within the scope of your project tender and assist you in meeting the objectives when writing your tender application.

Discover more about our Environmental Policy Consultation and Tender Support services.


We offer education and training in DNA-based monitoring, having accumulated years of experience in industry and academia. You can enhance your teams’ knowledge of eDNA and DNA methods and develop a more in depth understanding of how to apply these methods robustly alongside other tools to help address particular biodiversity monitoring challenges, with training from our team of globally renowned experts.

We will tailor training to suit your requirements and deliver over a method of your choosing, be it remotely, on-site, in person or as a blend.

Explore our training services and the impacts our collaborations have achieved.