How To Clean Salt Build Up In Hydroponics Systems

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By Chris Lipsey

It’s not uncommon for hydroponic systems to have salt build-up.

Salt accumulation makes it difficult for your plants to grow healthy and strong since the salt will end up suffocating them.

There are some very simple steps that you can take to easily clean salt buildup and flush out your hydroponic system so that your plant’s vascular system stays healthy, reducing the risk of mineral deficiency and giving you hydroponic plants you can be proud of.

Also Read: Cleaning Hydroponic Air Stones

How to clean salt build up in hydroponics systems in 3 simple steps

Follow the below steps to remove excess salts and maintain a clean hydroponic reservoir.

1) Water removal

Remove as much water as you possibly can from the reservoir before cleaning it out. This ensures that you don’t dilute your cleaning solution and reduces the time it takes to clean out your reservoir.

If you have a sump pump, consider using that instead of removing all the water yourself with buckets or hoses. A small submersible sump pump can help save lots of time when emptying your hydroponics system’s reservoirs.

2) Grab a bucket and stir

Fill a large bucket or any sized tub with water and add 1 cup of table salt into the water. Stir until the salt is completely dissolved.

Pour this solution into your hydroponics reservoir and let it sit for a few hours (try overnight). The next day, strain out all of the residue with a mesh strainer or cheesecloth to remove excess salts from your system.

Note: This step may require multiple rounds depending on how much water you have in your reservoir.

3) Cleanse your system

Pour your pre-made solution over every part of the equipment where there is still any standing water left behind. You can use a long handleled scrubbing brush or reguarl sponge to wipe down everything and flush out any remaining salt crystals.

When you’re done, turn on your water pump for at least an hour to put fresh nutrient-rich water through your system. Your hydroponics reservoir is now clean! If the process was too much work, consider hiring professional help, depending on how big your setup is.

Pro Tip: You can use distilled white vinegar and lemon juice to clean your system instead of table salt. These ingredients are very cheap and easy to get hold of, but you should still strain out the residue before adding fresh water.

Other ways to clean your system

There are some other options for cleaning salt build-up too:

  • Phosphoric acid – This is a liquid acid that has many uses including cleaning hydroponic systems. Just make sure to use the phosphoric acid rather than any other type of acid, because it won’t corrode your system like some others will do.
  • Cultured Solutions UC Roots – This is a special blend of beneficial bacteria for breaking down salt build-up in hydroponic systems.
  • Oxyclean – You can use this household cleaner to clean your hydroponic system, but you should mix it with water unless you want a bubbly mess everywhere.

Why is salt buildup a problem for hydroponics?

The reason you need to get rid of salt build-up is because you are growing plants with hydroponics, which means that they rely on the nutrients within the water of the system to survive.

If there is too much salt build-up in your hydroponic system, then this will affect the root system and limit how healthy these plants become. It may also impact their growth rate as well, which is why routine maintenance is suggested.

Learn more about problems and issues in hydroponics systems.

Signs of salt burn damage in plants

There are some easy-to-spot signs you need to look for if you suspect that your plants are suffering from salt burn.

signs of salt burn damage in plants

The first sign is browning of the tips and edges on leaves, which typically starts at the bottom of a plant closest to where nutrient solution is being absorbed by roots.

If it continues upward, further signs include curling or rolling of smaller leaves inwards towards stems with large fan-shaped leaves becoming smaller and thicker.

Necrosis of tissue can also happen in extreme cases, where leaves turn yellow or brown all over the plant and die off.

If this happens, you’ve got bigger problems to deal with than just your plants looking bad – there is a lower chance that they will ever recover from such an injury! The same goes for plants that are wilting despite having plenty of water.

If they don’t recover within a few days, you may want to consider replacing them with new ones or starting over completely if their roots have been damaged by excess salt in the solution.

What water should I use for hydroponics?

Tap water contains soluble salts, which is why it’s recommended that you don’t use it for hydroponics. Tap water often contains high levels of chlorine and fluorine, which can harm your plants by inhibiting their nutrient uptake ability.

The best type of water to use is reverse osmosis (RO) or distilled water. However, these types of water are expensive and difficult to obtain unless you have a home unit. If you don’t want to buy in an RO system, then use filtered water instead, which you can buy at your local store.

What are biofilms?

Biofilms are colonies of microorganisms that cling to surfaces. They are held together by a slimy layer, or matrix, which contains the microbes and their excreted wastes. Microbes form biofilm communities for many reasons:

  • Biofilms protect against environmental stressors such as changes in pH, light intensity, nutrient availability etc.
  • Biofilms provide a high surface area for microbial attachment and nutrient exchange between the microorganisms and their environment.
  • Some microbes within biofilm communities can switch from free living to symbiotic lifestyles, increasing each other’s survival rate.

Biofilms are very common in natural aquatic environments such as lakes, rivers etc., but also in man-made structures such as hydroponics systems.

A quick recap

Experienced growers will have their own set cleansing process (AKA a nutrient flush) in place, to keep their salt levels healthy. You should to, here’s a rundown of what we’ve discussed:


Flush water out of your hydroponic system once per month.


Use natural cleaning solutions if possible.


Add nutrient solutions to your clean water.


Check your plants pH levels and monitor any potential nutrient deficiencies by looking out for salt burn.