Flushing Your Hydroponic System: Water vs. Agents

By Chris Bond
Published: January 6, 2020 | Last updated: April 30, 2021 12:51:46
Key Takeaways

Whether or not to flush is not the question. This is as true for your personal bathroom habits as it is for your hydroponic system — flushing is a must.

Basics of Flushing

The flushing of any hydroponic system is done as a practical matter. Any operator of a hydroponic system that does not at least occasionally perform this measure will ultimately fail at growing anything due to the buildup of bacteria, algae, etc., that finds its way into even the most expertly managed hydroponic systems. Most systems, while they are in use, need to be flushed at a minimum of every one to two weeks. Some growers flush their system between crops; others do it every time or every other time they wish to add nutrients to their reservoirs. Frequency of flushing will be dictated by the needs of the system to keep it clean and the preferences of the individual grower.


In the decision making process of deciding to use agents, it is important to consider the reasons for using them. Most, and arguably all (who aren’t seeking the contrary for research purposes) growers would like to make sure their plants are integral components of healthy, living systems, thriving in a clean environment which reduces the incidence of disease pressure or other external stressors of plant health. Make sure to understand the differences between cleaning versus trying to eradicate all bacterial or microbial life. The difference between sanitation and disinfection is the difference between wiping things down to collect debris and using a product that acts as a bactericide, viruscide, algaecide, or other antiseptic.

Read also: Hydroponic Systems: Know When to Flush ’Em


In general, a flush of your hydro system between crops with some sort of chemical or biological agent should be viewed as an opportunity to kill anything and everything so nothing carries over between crops. If, however, you want to perform that same type of flush when there are still plants in the system, that approach will likely kill all your plants, but more on that later.

Flushing Agent Options

The range of products available to clean out your hydro system with a flush can be overwhelming. Arriving at a choice by asking what someone else uses may not help to narrow down your selection. Visit any message board on the topic and you will see almost as many different opinions on what to use and when to do it as there are individual growers. There are plenty of products and each can work for your situation depending on your system and budget.

There are many options for flushing your system that you may already have in your kitchen or bathroom. Some growers use simple hand or dish soap when they do a flush between crops. One drop per gallon is a common ratio for these DIYers. Other common and effective options include bleach or hydrogen peroxide — more on those below. Your media, however, may dictate what type of agent would work best for your scenario. If you use coco or stonewool, you may want to consider a flushing agent with enzymes to break down any dead root or other biomass that may have accumulated there.


There are growers who swear by using just water for flushing. They typically use reverse osmosis (RO) water, distilled water, deionized water, or any other aqua with a neutral pH (7.0). In an otherwise clean system, this may be all that’s required. Remember, though, you cannot see all the potential contaminants in a system. Just because it looks clean, doesn’t mean it really is.

Flushing With or Without Plants

If you notice plants in your hydro system are starting to look sickly or show signs of stress, you may be tempted to try and flush your system while your plants are still in it. Your plant leaves may be curling, getting brown spots, or if you accidentally add too much of a particular nutrient or are noticing some algae in your water — but your plants still look otherwise unaffected — it may be time to do an unscheduled flush. This can be done while your plants are still growing in the system if done carefully. Do not try to use any flushing agents not approved for use with plants if you are leaving your plants in place during a flush. The plants will absorb the chemicals and at best will kill them. At worse, it won’t kill them, but the plants will have absorbed the chemicals and the end consumer will end up eating them. If flushing with plants in your hydro system is the best course of action, there are a couple of options.


Read also: Preparing Your Plants for Harvest

Hydrogen peroxide can be used in a hydro system to increase the sanitation level and will not harm the plants. Hydrogen peroxide will help the plant by providing additional oxygen to the roots. This is true so long as the amount used is not excessive. Start with food-grade hydrogen peroxide which is usually in a 35 per cent concentration. Dilute this with 10 to 12 parts deionized, RO, or distilled water to reduce the concentration to about three per cent hydrogen peroxide. Add one to two teaspoons (five to 10 milliliters) of the diluted solution per each gallon (four liters) of water in your system. Adding vinegar is another possibility, but this can be tricky business if care is not exercised. Vinegar will lower your pH, so keep that in mind, but it won’t harm your plants if diluted enough. Dilute white vinegar down to a similar ratio of the hydrogen peroxide of one to two teaspoons (five to 10 milliliters) per gallon of water. Be prepared to adjust the pH accordingly, though.

Flushing Salt and Nutrients from Soil

Flushing is sometimes a necessary step in soil culture too. If salts have built up or the plant has received an overdose of nutrients, it can often be saved with a flushing of clean water if caught and acted upon in time. A volume of water at least three times the volume of the container is recommended to try and leach out the unwanted nutrients or other foreign substances. Plants grown in soil culture that do not get flushed when salts build up are prone to root rot or other diseases that will kill the plant or affect the yields.

Some growers flush their soil-grown crops as a matter of course during the last couple weeks of the plant’s bloom so that it will be sure to use up all its stored nutrients. They cut off the fertilizer supply or switch the irrigation to water only so that it cannot get any additional nutrients and will be forced to invade its stores. It is important to use pH-appropriate water during this phase, so plants can be sure to absorb all those available nutrients. Water with pH that is too high or too low can make the present nutrients unavailable to the plant even if the nutrients are there in sufficient amounts. If growing hydroponically and the grower wishes to do this, nutrients should be withheld for only the last couple of days pre-harvest.

Read also: Plants on Lockdown

In between crop cycles, the choice to use agents is up to each individual grower. In nature, the cycle of water flow usually does an adequate job of keeping things clean. A growroom or a hydroponic set-up is not exactly the spitting image of a diverse, thriving ecosystem. Cleaning agents such as bleach, hydrogen peroxide, vinegar, or any other number of commercially formulated agents will do a more thorough job of sterilizing your equipment and increasing its useful life.


Remember if you are using anything other than plain water, there are safety considerations. Just because a cleaning product is labeled as “natural” or “organic” does not make it safe to use. Fire can be natural and organic, as is quicksand, poison dart frogs, and salmonella. Be sure to read the label of any product carefully and observe any requirements for personal protective equipment and note the signal word (Caution, Warning, or Danger). When it comes to anything labeled as a pesticide, which includes many industrial cleaners, reading the entire label’s contents is not just good practice and common sense, there is a legal requirement to do so. Wear gloves when handling any cleaning material and if there is the potential for splashing on your face or eyes, wear safety glass or a face shield.

Keeping a clean, sanitary and, when appropriate, sterile system is critical for the health of your plants and those that might be eating them, but it is not worth risking your personal health to achieve it.


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Written by Chris Bond | Certified Permaculture Designer, Nursery Technician, Nursery Professional

Profile Picture of Chris Bond

Chris Bond’s research interests are with sustainable agriculture, biological pest control, and alternative growing methods. He is a certified permaculture designer and certified nursery technician in Ohio and a certified nursery professional in New York, where he got his start in growing.

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