Jun 24, 2026
Protocol for collecting water samples for eDNA 2026
- Katrina Lohan1,
- Emma Palmer1,
- Calli Wise1,
- Ruth DiMaria1,
- Lael Collins1,
- Tara Sill1
- 1Smithsonian Environmental Research Center, Coastal Disease Ecology Lab
- Coastal Disease Ecology Lab - SERC
Protocol Citation: Katrina Lohan, Emma Palmer, Calli Wise, Ruth DiMaria, Lael Collins, Tara Sill 2026. Protocol for collecting water samples for eDNA 2026. protocols.io https://dx.doi.org/10.17504/protocols.io.5qpvojx5dg4o/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
Created: May 27, 2026
Last Modified: June 24, 2026
Protocol Integer ID: 318016
Keywords: water samples for edna, collecting water sample, water for edna, water sample, sampling device, edna, protocol, sample, water
Abstract
This protocol describes how to collect water for eDNA either by hand or with a sampling device.
Guidelines
This protocol was developed with the assumption that the end-user possesses baseline knowledge of appropriate aseptic/clean techniques and a comprehensive understanding of the potential risks of contamination inherent to the workflow.
Notes on methodology:
This method is only recommended for experienced eDNA collectors as there are many points where unintentional contamination can occur. For novice collectors who wish to start incorporating eDNA into their projects or experiments, we recommend using products such as those sold by companies like Smith-Root which provide many self-contained eDNA filter options that limit risk of contamination for all users.
Notes on standard CDE clean techniques:
- If collecting the samples without the aid of a sampling device (i.e. by sticking the bottles in the water using your hands), it is imperative that clean gloves must be worn throughout collection. They need to be changed between sites for collection or IMMEDIATELY after any part of the sample has been touched. Gloves are optional when using a sampling device, though they are recommended.
- The only parts of the water collection bottles that should be touched are the outsides of bottles and lids. At no point should your gloves or hands contact the inside of the bottles, the inside of the lids, or the water inside of the bottles.
Materials
- 1L pre-sterilized & labeled Nalgene bottle
Note: Total = number of samples * number of replicates + number of field days
- Sampling devices (1 primary and ideally 1 back-up)
Note: This is typically a long pole with a way to attach a sample bottle(s) on the end
- Nitrile Gloves (at least 1 pair/site)
- Large cooler(s) filled with ice with sufficient space to hold all the bottles needed for the day
Safety warnings
- Chlorine bleach is routinely used to sterilize surfaces and equipment. Bleach is an oxidizer and corrosive. The active ingredient, sodium hypochlorite, is incompatible with several reagents and chemicals used in the laboratory. For more detailed information, refer to the Sodium Hypochlorite (Bleach) Safety Fact Sheet.
- Diluted bleach solutions must be made fresh each day they are needed to ensure the proper concentration is applied for sterilization purposes. Diluted chlorine bleach breaks down into water and salt within 24hrs.
Pre-Sampling Preparation
Bleach clean the sample bottles following the Sterilization Techniques protocol. This is best done before shipping to the field site, especially if the bottles do not need to be reused across sites.
Pre-label the bottles with the site and sample (and field replicate if collecting two replicate sample bottles per sample).
Note: The CDE lab typically collects 2 1L replicate bottles per sample in the field (1 for filtering and 1 as a back-up).
Field Collection
If collecting the samples by hand (i.e.without a sampling device), wear clean gloves throughout the collection, changing them between sites or anytime the gloves become dirty. Gloves are optional when using a sampling device, though they are recommended. Some sampling devices can collect two bottles at a time for which the protocol is identical.
Before heading out into the field, fill the field control with water (ideally DI water but can be tap in a pinch) and place it in a large cooler filled with ice and the other eDNA bottles.
Note: One field control is necessary per field day. After being filled with water, the field control should otherwise act as a sample by being taken out into the field and transported back to the lab along with the other samples. This is the only field control required for this kind of eDNA sampling.
Once you have arrived at the collection site, put on clean gloves if required.
Strap the eDNA bottle into place if using a sampling device OR grab the eDNA bottle with a clean glove.
Using the glove, unscrew the cap and leave it face-up someplace safe.
Downstream of your sampling location, triple rinse the bottle in the water by filling up the bottle and then dumping it out on the other side of the boat or somewhere else far away from the collection site.
Upstream of where you triple-rinsed, collect your sample by filling the bottle completely. If using a sampling device, be careful not to tip the bottle over while bringing it back to the boat.
Note: If collecting the bottle by hand, keep the mouth of the bottle pointed upstream while collecting.
Screw the cap on and place it in the cooler full of ice.
Continue until all field replicates and samples at the site have been collected.
Change gloves before collecting samples at the next site.
Once all the collections have been completed, the water can be filtered with either a peristaltic or vacuum pump following the appropriate protocol.