Hydroponic Systems: Know When to Flush ’Em

By Frank Rauscher
Published: September 1, 2016 | Last updated: April 27, 2021 12:05:36
Key Takeaways

Hydro growers need to know about flushing, both why they’ve got to do it and how they should go about it. But what are you really flushing, exactly? Your plants, your system or both?

Source: Irochka/

There are two main reasons to flush a hydro system. You’re either flushing to clean out the system, or to rid your plants of excess nutrients. There are major differences between a plant flush that happens sometime during a crop’s cycle, and a cleaning flush that takes place between crops.


There doesn’t seem to be much debate over a cleaning flush, but consensus over a plant flush is a different story.

Flushing Between Crops

Cleanliness is always very important in keeping the plants in a hydroponic system healthy. It is normal for the water reservoir, feed lines and pump in a hydroponic system to stay wet throughout the grow cycle.


This is adequate time for various fungi and bacteria to get a foothold. We know there are beneficial microbes, but the concern here is pathogenic or harmful microbes, which tend to grow right along the beneficial ones, especially if the system may be low in some of the beneficial populations.

On top of micro-organisms there is also a buildup of nutrients, nutrient by-products and salts occurring in your system, which is a big reason flushing is recommended at the end of every crop cycle.

Nutrition levels in the water can be checked, but the levels at which nutrient levels may be in the grow media are difficult to ascertain.


Because of this, and because knowing how much and which nutrients pre-exist in the system, a good cleaning, flushing and rinse are essential for getting the most of your next crop and minimizing any taste or health problems.

Algae are another big concern. An alga infestation is not usually bad enough to kill off your plants, but this form of life feeds off the same nutrients your plants need and so reduce crop yield.


It is often likely that the alga is not present in sufficient quantities to see, but there are enough of them to affect yield and health.

Proper maintenance and a good-quality filter can minimize the presence of algae, and so can a good flush. Remember that algae also compete for oxygen in the water, yet another reason making sure each new crop starts off clean is important.

The condition of your grow media, reservoir, pump, feed lines and drip emitters is critical for maintaining plant health.

When performing inter-crop cleansing, consider each of these items. Often old grow media is discarded as it may seem too cumbersome to clean thoroughly. There are several products and techniques out there for flushing your system.

Check them out! One very important issue for drip emitters is buildup of salts or living organisms like algae.

Quality rinse products are available to deal with emitter plugging and when used properly will keep your emitters working properly for many more crop cycles.

As the many techniques for cleaning these various systems parts are beyond the scope of this article, scan the QR code at the end of this article to explore some of these.

The bottom line is, when starting off each new crop, try to get your system and media as close to clean and disinfected as possible.

Make sure you have removed all traces of disinfectants and re-established the right beneficial microbes. Disinfected grow media is a goal, but so is maintaining a living soil or water system.

So, after cleaning and disinfecting, make sure to remove cleaning agents with ample fresh water, allow air (oxygen) to do its part by letting it dry, and follow with re-establishing the beneficial microbe levels.

Flushing During the Grow Cycle

When researching this aspect of crop care, you will find there are strong opinions on each side of the issue.

Some researchers claim they find no study documenting the claims and benefits from rinsing or leaching during a crop cycle, while at the same time I could not find a study that showed it to be ineffective.

Many growers believe that starving the plant for nutrition during its final phase (roughly 10 days before harvest) diminishes the amount of nutrients held in the leaves, making them tastier specimens. However, the same amount of growers do not believe this to be true.

As with most technical debates, I tend to think there are facts to support both sides. I can imagine that this rinsing or leaching process is most effective when the level of nutrition being provided in the first place is rather high.

Finding salt damage to the foliage where plants are overfertilized or simply where the salts have built up over time is not unusual.

Correcting this over-fertilized state is almost always accompanied by a recommendation to flush or leach the soil. In an attempt to maximize growth, it is not unusual for a grower to apply more fertilizer than what might otherwise be recommended.

This would warrant a flushing of sorts. There could be other reasons that justify a flush prior to harvest, but the dispute and disagreement is strong. On this point I was not able to find any study comparing these practices.

What about slimy roots? – If you can see and feel slimy roots in your system, you will need to clean them as soon as possible by doing a thorough rinse followed by a media flush. Treating the infected roots with a diluted dose of hydrogen peroxide can stop the infection. Disinfecting your system between crops will help minimize the opportunity for this condition to get started in the first place.

What about senescence? – Plants have a natural aging cycle. Take the changing color of leaves in the fall, for example. The plant is removing nutrients from some of its leaves and then storing this energy in the roots. Senescence includes more than just this process.

Some plants are annuals living only one season, while others are perennials that live on for several. Storing energy in the roots is a critical process for perennials and a part of aging. This same aging process is important in the annuals we grow for food.

As we usually want certain aspects from our veggies that would not be available if they were allowed to completely age before harvest, we intentionally interfere with senescence.

The goal for the plant is to set seed and then reproduce. Flushing allows growers to alter the taste or other features of their crop at some point before harvest, which is in complete keeping with conventional agriculture.

What about salt buildup? – When growing ornamental plants in the landscape, salts will build up over time, and leaching or flushing can make a big difference towards the health and vigor of the plants. Fruit trees will also benefit from flushing when they have been subject to high levels of total dissolved solids (TDS) or poor drainage.

Salt buildup on the roots is detrimental. For many hydroponic edible crops, their life cycle is short in comparison to soil-grown crops, and if there has been no buildup over time, rhizosphere salts should not be a problem.

If the application of nutrients is high, however, the salt index in the soil or grow media will also be higher and it may be likely that high salts are present. Flushing reduces this.

Crop Flushing Timing

As far as verifying that flushing indeed works, tissue samples can be taken from the leaves of plants in a control study to find out just how much remaining phosphorus and nitrogen there is following a thorough rinse. This could provide some much-needed insight on this aspect, yet studies remain limited.

For the present, let’s assume that where heavy feeding is practiced, cutting off the nutrient regimen and flushing the rhizosphere will aid in the reduction of nutrient levels found in the foliage and have an impact on the flavor of said foliage.

If this is a practice you wish to follow, then flush during the dark cycle so that your plants are much less likely to take up any flushing additives you may be using. In general, plants are far less active in darkness when their photosynthesis process is not active.

When edible plants are subjected to heavy fertilization, which may be practiced in the attempt to gain in crop mass or vigor, salt buildup can occur.

This buildup can lead to nutrient lockout, and consequently symptoms of undernourishment will begin to appear. Because of this, routine or occasional flushing can benefit a plant, and not just in the last 10 days of growth.

When this leaching is done earlier in the growth cycle, it should immediately be followed by a healthy, well-balanced shot of fertilizer to re-establish appropriate nutrient levels.

Whenever you plan on flushing, don’t forget about your beneficial microbes. Their numbers will be reduced during a flush and should be replenished.

As you might assume, the pathogenic microbes will also be reduced, and as you will not be replenishing them, the good-to-bad ratio will be improving significantly.

Flushing and cleaning your systems is an important part of a healthy crop. Whether it’s done before or during the growth cycle, when and why you decide to do this will be based on factors that are occurring within you crop.

As you inspect your plants, take notes and then perform actions to correct any negative symptoms. Growing is fun and the challenges only make it more interesting.


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Written by Frank Rauscher | Writer, Owner of Garden Galaxy

Profile Picture of Frank Rauscher
During his many years of service in horticulture, product development and sales, Frank has performed innumerable visits to landscapes to facilitate a correction for struggling plants or assist with new design. He also writes for Southwest Trees and Turf and The Green Pages, is the owner of Garden Galaxy and manages several websites. He has four children and eight grandchildren.

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