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This page provides an overview on the topic of produce safety in hydroponic and aquaponic operations, discussing the ways in which water, systems, people, and fish can impact produce safety. It also includes tables of specific produce safety factors and related action items for growers, with links to more specific resources. These are organized by topic area:


Produce safety is meant to reduce and prevent contamination of produce with harmful human pathogens, such as bacteria, viruses, and parasites. This is done by controlling known risks. Other factors to be aware of include mechanical and chemical contamination, but this guide will focus on human pathogens.
Hydroponic and aquaponic production are unique, from a produce safety perspective, because of the way water is used, the specific constructed production systems in use, and how people are involved in the systems. Aquaponic systems have added produce safety considerations related to the inclusion of fish.



Hydroponic systems use stored and/or circulating nutrient rich water in greater volumes than other forms of production which presents unique produce safety circumstances. This is sometimes referred to as “nutrient solution” since it is “production water” that has nutrients added to it. For the purposes of this document, these terms mean the same thing.

Nutrient Rich

Water delivered to the plants is full of nutrients, since this is the source of food needed for plant growth and crop production. Since human pathogens depend on water and food to survive and reproduce, there is a chance that this water can be contaminated with them.


The very nature of hydroponic production means that water is central to plant growth. This is true of other production systems, of course, but in hydroponic systems the potential for contact between production water and the edible portion of the crop is greater.


In most hydroponic systems, the water is also circulated.  This means that contamination in one place can quickly spread to other places and, perhaps, through-out the entire system.

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Hydroponic production depends on constructed systems which introduce unique food contact surfaces in the growing environment.

Food Contact Surfaces

Because hydroponic production doesn’t involve soil, other growing media and structural surfaces such as rafts and troughs are used. The media and support surfaces can become “food contact surfaces” due to the way plants grow and how the surfaces are handled. This requires special attention to these surfaces relative to cleaning and sanitizing. The abundance of nutrient rich water and its circulation also leads to connectivity between different parts of the system. For example, any surface that the recirculated water contacts should be treated as a food contact surface if the water later has the potential to contact any harvested food, or other food contact surface. The water connects all these surfaces.


Product movement is unique in hydroponic operations as well. Sometimes rafts and troughs are moved prior to harvest. Other times, the primary movement is at harvest time. Regardless of the timing, it is important to take care when moving parts of the production system to prevent water dripping and contacting food contact surfaces or the harvested portion of the crop. Common examples to consider are:

  1. lift each raft for harvesting in such a way that it does not drip production water over produce, other rafts, or other food contact surfaces, and
  2. lift rafts out of the water in a way that prevents edges or corners from dipping into the production water which can lead to contact between production water and produce or food contact surfaces.

Cleaning and Sanitizing

Given the considerations above, it becomes clear that cleaning and sanitizing food contact and water contact surfaces is critical for control of human pathogens (and plant pathogens). Unfortunately, many of these surfaces are not well designed for cleaning and sanitizing. So, there is a need to carefully document appropriate standard operating procedures (SOPs), appropriate cleaning and sanitizing tools and supplies, and think about continuous improvement through the application of hygienic design principles.

Watch as this Quick-Cut Greens Harvester gets cleaned and sanitized:


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Due to continuous and high levels of production, hydroponic production tends to involve more human contact during the plant growth period. Growing surfaces are moved, water is managed, and harvest involves movement of product and surfaces by people.

Procedures and Practices

Hydroponic operations tend to involve significant human interaction during the period of plant growth and in other ways that can result in contamination. Moving germinated plants to production surfaces, moving production surfaces through the production system, managing water supply, water treatment, and harvest occurring in or near the production area all tend to lead to human interaction with the system. Even cleaning and sanitizing of water contact and food contact surfaces, when not done completely, can present risk. These activities should be carefully planned and described so that each person completes them without introducing the risk of contaminating the system with human pathogens.

Worker Health and Hygiene

Not working when sick, hand washing before and after contact with produce, water, or food contact surfaces, and ensuring all workers are trained and aware of produce safety risks and best practices are all measures that can reduce contamination risk.


This guide is meant to provide an introductory overview of key produce safety considerations for hydroponic growers. The table below provides specific items to discuss with your team and to act on as you develop a produce safety culture and plan. More specific resources are available below.

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Nutrient Solution / Production Water

Watch as Jordan Miranda of Legacy Greens in Tallahassee, Florida, describes how they change out the production water and clean their systems, or what they like to call a "rez change."


Produce Safety FactorWhat You Can Do About ItResources

Nutrient Solution/

Production Water


  • Track water quality parameters over time
  • Filter and/or treat nutrient solution
  • Maintain farm hygiene / biosecurity

Note: Resources for aquaponics or terrestrial aquaculture are often adaptable to hydroponic and/or aquaponic operations. For example, the Daily Water Quality Log for aquaponics can be adapted for hydroponics by removing the column headers that aren’t relevant and adding in parameters that are.

Nutrient Solution/

Production Water

Contact with


  • Prevent contact through system design and crop choice. If contact occurs, nutrient solution is agricultural water and must be maintained according to the FSMA Produce Safety Rule. If contact occurs during or after harvest, maintain water quality according to the more stringent requirements for postharvest agricultural water in the FSMA Produce Safety Rule.

Nutrient Solution/

Production Water

Contact with

Food Contact


  • Prevent contact where possible. To mitigate, clean and sanitize the affected surfaces before using again.



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Cleaning and Sanitizing

Read this guide: Cleaning and Sanitizing for Hydroponic and Aquaponic Operations

Produce Safety FactorWhat You Can Do About ItResources


  • Effectively clean surfaces prior to sanitizing.
  • Establish and follow a cleaning schedule and use standard operating procedures to ensure cleaning happens as needed.
  • Prevent cleaning activities from contaminating produce. For example, avoid using a pressure washer to remove algae from the production area floor while in production.
  • Consider buildings, transport equipment, trash, litter, and waste in a cleaning plan.
  • Keep production and packing areas tidy to increase efficiency and reduce the risk of a pest infestation.
  • Use the right tool for the job and consider color coding of tools for specific tasks to prevent cross-contamination.

Choosing a Sanitizer

  • Streamline operations by using one product approved for all uses, being clear about different application procedures with labeling, training and SOPs; or,
  • Intentionally choose specific products for different uses and clearly communicate this approach with staff through training, labeling, and SOPs.
  • Determine appropriate dose of sanitizer for the intended use.
  • Take care when measuring and dispensing sanitizers.


  • Identify the 4 zones: Food contact surfaces (Zone 1) and adjacent surfaces that could indirectly contaminate produce.

Note: Resources for packing houses are often adaptable to hydroponic and aquaponic operations.

  • Regularly inspect, maintain, clean, and, when possible, sanitize Zone 1 (food contact) surfaces.
  • Establish a cleaning and sanitizing schedule tailored to your operation, making sure to prevent re-contamination of sanitized surfaces through other cleaning activities.
  • Use water of adequate and sanitary quality for diluting and applying sanitizers (must meet FSMA PSR requirements for postharvest agricultural water).

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Harvest and Postharvest Handling

Read this guide: Harvest and Postharvest Handling for Hydroponic and Aquaponic Operations

Produce Safety FactorWhat You Can Do About ItResources


  • Lay out the harvest process to reduce the potential for cross-contamination of produce, tools, and hands through production water.

Note: Resources for packing houses, like this one, are often adaptable to hydroponic and aquaponic operations.

  • When harvesting and packing crops with roots attached, consider steps to reduce the opportunity for cross-contamination between water and produce, such as using containers to keep roots separate. If water and crops come into contact, production water must contain no detectable generic E. coli in a 100 mL sample.

Washing Produce

  • Consider whether washing your produce is necessary for product quality. Most postharvest washing is done to remove soil and debris from the field, and in many HP/AP operations this is not a significant issue. Also, washing of harvested produce is not required by the FSMA PSR but can be a part of certain market requirements.
  • Use sanitizer when washing produce to prevent cross-contamination.
  • Manage and maintain wash water quality to ensure the effectiveness of the sanitizer.


  • Clean and sanitize storage areas before use and on a regular schedule to prevent contamination of the produce.
  • Prevent condensation from dripping on to harvested produce.

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Personal Health and Hygiene

Read this guide: Personal Health and Hygiene for Hydroponic and Aquaponic Operations

Produce Safety FactorWhat You Can Do About ItResources

Washing Hands

  • Create an SOP that describes when and how workers must wash their hands.
  • Train personnel and check compliance with hand washing procedures regularly.
  • Post instructional signs at handwashing sinks, in languages that personnel can understand.
  • Harvest is a key moment for potential cross-contamination through hands. If one person is doing multiple steps in the harvest, they must wash their hands before handling the produce. For plant health and biosecurity, it’s a good idea to wash hands before and after touching system components, e.g., foam rafts, as well.

Visitors and Volunteers

  • Visitors who don’t touch the production system must be made aware of the farm’s food safety policy.
  • Visitors or volunteers who interact with the system, especially edible or harvestable portions of produce, must be fully trained in the farm’s food safety procedures as if they were a regular employee doing the same job.

Sick Personnel


  • Train workers in health and hygiene practices and do not let sick personnel handle produce or touch food contact surfaces.
  • Provide paid sick leave for workers with gastrointestinal illness.

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Wildlife and Domesticated Animals

Read this guide: Wildlife and Domesticated Animals in Hydroponic and Aquaponic Operations

Produce Safety FactorWhat You Can Do About ItResources

Pest Animals

  • Conduct and log regular scouting for animal damage to crops and other signs of intrusion, including feces.
  • Conduct preharvest crop assessments to look for evidence of potential animal contamination in open-air and partially-enclosed operations.
  • Exclude pest animals in fully-enclosed (indoor) operations.
  • Place rodent bait boxes, when used, on the exterior, not interior, of structures.

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Produce Safety FactorWhat You Can Do About ItResources


  • Plan out audits over time based on market and operational requirements.

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Fish: Aquaponic-Specific Considerations

In addition to water, systems, and people, as described above, aquaponic operators must also consider the potential produce safety impacts of fish. In an aquaponic operation, the production of fish and produce are interconnected through recirculating water. Practices that promote an aquatic environment that will support the growth of healthy fish impact produce safety.  Because the produce and fish p production pieces of an aquaponic operation are interconnected, establishing a system and maintaining practices that support fish health and proper handling will also promote produce safety.

Read this guide: Fish Health and Handling for Hydroponic and Aquaponic Operations

Produce Safety FactorWhat You Can Do About ItResources


Fish Care


Produce Safety

  • Support healthy fish to reduce produce safety risk.
  • Design the fish unit to actively manage solid waste so that it doesn’t accumulate in system components.
  • Start with fish that have been quarantined and a system that has been thoroughly cleaned and sanitized.
  • Establish standard operating procedures, especially around hygiene and biosecurity, to ensure that human-system interaction does not become an opportunity for cross-contamination between the outside environment, the system, and produce.
  • Track water quality parameters as a component of routine fish health assessment.

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Ongoing Work

In 2022, NECAFS received funding from the USDA NIFA Food Safety Outreach Program (FSOP) to continue working in the area of hydroponic and aquaponic produce safety. This project has five primary objectives:

  • Advisory Group - Form a nation-wide hydroponic and aquaponic produce safety advisory group that informs project outputs at multiple steps.
  • Needs Assessment - Determine produce safety educational needs and gaps specific to hydroponics and aquaponics.
  • Educational Resource Development - Develop educational curricula, programs, and resources for diverse audiences with interests in hydroponic and aquaponic produce safety.
  • Education Delivery and Evaluation - Deliver educational resources and programs to relevant audiences and evaluate outcomes and impact.
  • Coordinate Future Research - Coordinate research efforts to address knowledge gaps.

This 3-year project has begun with the formation of Advisory and Collaborator groups to help direct and plan the work. An initial needs assessment is being conducted to further focus educational curricula and program development. This process will also inform a research roadmap to direct future research to address identified gaps in knowledge.

If you would like to receive updates on new educational resources and programming, please don't hesitate to reach out to Sean Fogarty at sean.z.fogarty@uvm.edu. We also welcome those interested in becoming more involved by contributing to the advisory group, making connections between the project and growers, or collaborating on specific project activities.

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Intended Audiences

The intended audiences for these educational resources are primarily educators, regulators, technical service providers, and growers. The resources are written to guide the reader through produce safety considerations relevant to different aspects of hydroponic and aquaponic operations. The goal is to increase the knowledge of all stakeholders on this topic so that they can help guide produce safety practice implementation among hydroponic and aquaponic operators.

Intended Use

  • These resources are intended to supplement, not replace, existing resources and training.
  • They are intended to serve as a starting point for produce safety practice implementation and describe information specific to certain aspects of hydroponic and aquaponic operations where initial questions commonly occur.
  • It is assumed that the reader understands the FMSA PSR and food safety principles. Therefore, these resources do not duplicate existing content that covers produce safety practices consistent across agriculture (i.e., the principle of proper handwashing). Instead, they describe practice implementation specific to hydroponic and aquaponic system components and operations.
  • These resources are not exhaustive and are intended to provide a starting point for produce safety practice implementation in hydroponic and aquaponic operations.
  • Educators, regulators, and technical service providers are encouraged to share these resources with producers as appropriate.


This project was undertaken by NECAFS in direct response to feedback from network partners.


NECAFS, housed at the University of Vermont Extension, is one of four USDA funded regional centers tasked with coordinating training, education, and outreach related to the FSMA PSR and the FSMA Preventive Controls for Human Foods (PCHF) Rule. NECAFS’ work focuses on coordination and facilitation of the Northeast regional network to support a national food safety training, education, extension, outreach, and technical assistance system among small and medium-sized producers and small processors.

This work was led by Chris Callahan, Elizabeth Newbold and Sean Fogarty at NECAFS with the support of our Project Team and Advisors, whom we thank for the time, expertise, detailed review, and feedback they provided to this work.

  • Elizabeth Bihn
  • Davis Blasini
  • Audrey Draper
  • Laurel Dunn
  • Bradley Kai Fox
  • Laurie George
  • Todd Guerdat
  • Peter Konjoian
  • Chris Obergfell
  • Robson Machado
  • Meredith Melendez
  • Patricia Millner
  • Allen Pattillo
  • Lisa Rhoden
  • Camila Rodrigues
  • Sujata Sirsat
  • Michelle Smith
  • Phillip Tocco
  • Simon Yevzelman

The list of Collaborators involved in this work is ever-growing, and we would like to acknowledge those who have contributed to the project work through farm tours, Delphi study participation, and Super Fan group participation and contributions. Their openness to partnering with us makes this project possible.

Factsheet graphic design by Kelly Collar, Mad River Creative. Many thanks for working closely with us through several rounds of revision.

This work was supported by the Food Safety Outreach Program grant nos. 2018-70020-28878, 2021-70020-35497, and 2022-70020-01715 from the USDA National Institute of Food and Agriculture. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture.