Using eDNA To Estimate Fish Populations

By on February 27, 2023
Eastern Brook Trout. Eastern Brook Trout. (Credit: USFWS, via Flickr Public Domain)

Historically speaking, fish abundances have been assessed by catching a large number of fish from areas throughout the habitat and then making estimations based on the number of fish caught. However, this is not always precise as the fish could be concentrated in some areas, making it appear that the population has declined when, in reality, they may have just relocated. This method can also be time-consuming and expensive as it requires repeatedly netting and counting the fish.

Despite the drawbacks, population surveys and estimation are important and not something that can simply be ignored. Resource management agencies invest a great deal of time, money and energy into stocking fish and monitoring conditions in local water sources–population surveys are used to quantify the success of these efforts. 

Using eDNA to Assess Biomass and Fish Populations

Fortunately, advancements in research have led to the implementation of Environmental DNA (eDNA) as a tool for assessing populations. eDNA essentially refers to evidence of fish in the waterway–or anything left behind as they swim, forage and mate. While granted, “population” is not exactly the term used, but rather, biomass, eDNA can be used to indicate fish abundances. A 2020 study published by the Estuarine, Coastal and Shelf Science Journal explains that biomass is “the weight (whole-body, wet weight) of the in-water part of a fishable population.” In short, it can be used as a way of providing a measure of the quantity of fish as well as species diversity.

Using eDNA to assess fish biomass has many applications, ranging from assessing the success of stocking efforts to searching the water for the presence of invasive species. eDNA can be found in all major waterways, making it an accessible and important tool for population studies. A 2016 study conducted by scientists from the Universite Laval and Quebec’s Ministry of Forests, Wildlife and Parks looked at lake trout populations in 12 lakes throughout the Canadian province of Quebec.

This study was unique in that they had previously accepted data to compare their findings to. The old data had been garnered from the netting and extrapolating method, but if the eDNA method results were comparable, then fishery researchers could switch to the cheaper option. 

Much like how the old netting methods were done, the researchers collected eDNA from different parts of the lakes. At each sampling site, they gathered 10 one-liter samples from each lake, with each coming from a different part of each lake. Researchers then filtered the water and subjected the particles to genomic analysis techniques to accurately measure the quantity of lake trout DNA. They found a strong correlation between population estimates obtained using the traditional approach and those based on the new eDNA technique.

Additionally, the variations in eDNA abundance were found to be similar to those reported for net catches. This means that the new method can provide results just as accurately and reliably as the netting method but at a potentially much lower cost.


The success of the study in 2016 was one of many that led to the further use of eDNA in fishery research. Today, eDNA is commonly used for lake, river, stream and even ocean research. The capabilities of eDNA as a tool for fish population research are vast and can help minimize the amount of time and money spent arduously catching and counting fish. Though some organizations still use netting and other, more traditional methods, they are often paired with eDNA analysis to fill in any gaps and reinforce results.

Full results of the work are published in the Journal of Applied Ecology.


  1. Jim Ninos

    May 10, 2023 at 1:21 pm

    My name is Jim president of the Grass Lake Association and we have experienced a substantial decrease in our fish population on the lake. We also have a stocking program by the NYSDEC of tigar musky’s and our association has stocked fingerling walleyes along with DEC fry.

    We need to determine the effects of our efforts

    Jim Ninos
    We would like to sample the lake

    • Samantha Baxter

      May 16, 2023 at 2:52 pm

      Hi Jim,
      As far as sampling eDNA goes, USGS has a helpful resource on collecting the samples themselves. The process will also depend on which sampling kit you get. Actually extracting results is a bit more difficult. Here is a source that lists some of the labs you can process your samples through. Good luck!

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