Are your plants or soil waterlogged? There are many ways this can happen, but you CAN avoid losing your precious plants!

Waterlogging in Plants: There are solutions to save your plants from drowning, disease and contamination

There are solutions to save your plants from drowning, disease and contamination


What is waterlogging and why does it occur?

Waterlogging is when the soil and root zone around plants becomes saturated. Basically, the water can’t drain away fast enough. This occurs when more rain falls than the soil can absorb or evaporate into the air. This can happen with an intense period of rainfall such as summer storms. You may live in a heavy rainfall area and have a seasonal problem. If you live on a slope and have neighbouring properties above you, you literally may have water flowing through your garden.

Gardens and plants don’t only suffer from waterlogging as a result of extreme weather events. Overwatering especially in pots, poor drainage and heavy clay soils can also contribute to this problem.

What Happens when Soil and Plants are Waterlogged?

  • In healthy soil, there are lots of little air pockets around the soil particles. When these are saturated with water, the plant’s root tissues start to die off from the tips. The plant is starved of oxygen and carbon dioxide can’t move away. This can cause a toxic soil environment.
  • If you are just having a seasonal rainfall problem, this is unlikely to occur, unless the soil is waterlogged for a long period. Usually the excess water finds a way to escape before this happens.
  • It also depends on the type of soil structure you have. Heavy clay soils hold water for long periods as they have poor drainage properties.
  • If your waterlogged soil is caused by factors like poor drainage or overwatering, your plant may eventually die. Carbon dioxide and ethylene gases can build up in the soil around the plant roots. These gases can negatively impact root and plant growth.
  • Plants are also likely to become nutrient-deficient due to leaching. If your plants are starving, this can weaken them and they may attract pests and disease problems.

Don’t stress though. You can identify if you have a waterlogging problem and there ARE solutions!

10 Signs your Soil is Waterlogged

How do you know if you have a problem with waterlogging? Here are ten clues or symptoms to watch out for:

  1. Plant leaves may turn yellow. This may be due to nitrogen leaching out of the soil. The leaves may discolour in other ways. e.g. evergreen leaves may turn brown.
  2. Your plants start wilting, dropping leaves, shoots die back or leaves start to soften all of a sudden.
  3. Algae may start living on top of the soil in your pot plant or garden.
  4. Weeds like dock may appear. They thrive in an anaerobic (low oxygen) soil and arrive to help return health to your soil.
  5. Soil may start to smell ‘sour’ or become anaerobic. This is a clue the plant roots and aerobic microbes may be dying off.
  6. Water is pooling on top of your soil.
  7. Your plants are being attacked by pests or disease.
  8. Worms are coming up to the surface in great numbers (they are trying to save themselves from drowning)! Look for birds suddenly appearing for a free feed.
  9. You might notice a scum or residue on the surface of the soil.
  10. If you lift your plant out of the pot or soil, the roots may be discoloured and a dark brown or black. They may be suffering from root rot.

Waterlogged Plants: Your pot plants will show tell tale signs there is a problem with the soil or potting mix.

Your pot plants will show tell tale signs there is a problem with the soil or potting mix.

How to Prevent & Manage Waterlogged Soil

  • How do you restore and clean up plants that may have been contaminated by flood waters?
  • How do you revive plants that have been affected by heavy prolonged rainfall?
  • How do you fix soil that is badly waterlogged?
  • What can you do to prevent waterlogging in plants occurring again?

I’ve had to have my own strategies for coping with subtropical weather events, so here are some practical solutions and techniques to help you.

How to Treat Pot Plants Inundated by Flood Water

  • Firstly, hose off the plant foliage to remove any sludge or chemical residues. Use higher pressure for strong shrubs and potted trees and lower water pressure for delicate plants.


Waterlogging Tip: Use higher pressure for strong shrubs and potted trees and lower water pressure for delicate plants.

Use higher pressure for strong shrubs and potted trees and lower water pressure for delicate plants.


  • If the pot has accumulated sludge from the flood waters on top of the soil or mulch, remove it. Make sure you use gloves for protection in case of bacteria, chemicals or toxin residues. Bag this up and bin it.  You don’t want this contaminating other parts of your garden or coming in contact with humans or animals.
  • Next, scrub the outside of the pot and rim with warm soapy water.  Use a safe biodegradable or environmentally friendly soap, not one with chemicals. If the pot surface is porous, it will absorb these and they may end up in the soil.
  • It is likely the beneficial microorganisms and soil life that were living in your pot and keeping your plant healthy, have drowned. At best case, their numbers are likely to have been greatly reduced.  If this is the case, the potting mix or soil may smell ‘sour’ or anaerobic. Oxygen normally fills the gaps in between the soil crumb structure. All organisms and plants need air to live.  When plant roots start to decay, you may notice this unpleasant smell.
  • If the pots contained edibles that are close to harvest, it may be best to avoid eating these in case they were contaminated by pollutants.

Solutions to Restore your Soil and Plant Health

  • If you don’t want to re-pot the plant and the soil is still smelly, you can try sweetening the soil. Add a sprinkling of garden or agricultural lime to help remove the odour. If however, you have a plant that prefers an acidic soil, then avoid this treatment.
  • If you are prepared to re-pot your plants, then you can re-use some of the potting mixHowever, add some other ‘ingredients’ to build up the health and restore aeration. Ideally, remove any contaminated potting soil and put it through a hot composting system. This should remove any pathogens.Make sure you use gloves and a mask when mixing up the soil. Add equal parts of fresh compost, worm castings and if possible, vermiculite to retain minerals and aerate the potting mix.  Grade 3 Vermiculite (a puffed natural mineral called mica) is a good size and helps aerate plant roots. Alternatively use a coarse washed river sand available at landscapers for very low cost.
  • Remove any dead or dying shoots or foliage with clean secateurs.  Pay attention to tool hygiene. Ensure you wash your tools in warm soapy water if they have been used on sick plants.
  • If you are not re-potting, you can add beneficial microorganisms back into the soil. Gently fork in some fresh compost and/or worm castings into the top layer of the pot. Try not to disturb the roots of the plant.  Then ‘feed’ them with a drink of diluted molasses and seaweed or kelp.  Molasses is a thick black liquid that is basically a simple sugar that beneficial soil bacteria go crazy over at their ‘dinner table.’  It is usually sold cheaply at health food and garden produce stores and is a great investment in soil and plant health.  A capful in a watering can is all that is needed.  Follow the directions for the dilution of the seaweed/kelp.  Once the microbes have some food, they will have enough energy to start to multiply and get to work in your pot or soil. They will soon help restore the pH balance and plant health.  Repeat this treatment every 2 weeks until the plant recovers and soil health is restored.
  • Use a moisture meter to measure how much water is still in your soil. Moisture meters are a valuable diagnostic tool.  If the soil moisture measures above 80%, it is still too wet, so let it dry out before adding any more water.  The ideal moisture level is between 40% and 70%, which allows some oxygen to stay in the soil. Water when the soil moisture drops to <30%.


Waterlogged Plants Tip: Moisture meters help you know when your plant needs watering and when to leave it alone!

Moisture meters help you know when your plant needs watering and when to leave it alone!

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  • Finally, check the drainage holes at the base of the pot. Make sure the drainage holes are free of roots or blockages so water can drain away freely.  If your pots get waterlogged frequently, consider drilling more holes in the pot or transplanting into a more suitable container. You can also add some fine mesh like flyscreen to the base of the pot to prevent the drainage holes becoming blocked. Or put the pot up on feet or a portable trolley to enable water to drain freely.


Waterlogging Tip: A plastic pot like this has adequate drainage holes but some pots only have one at the base and may be blocked

A plastic pot like this has adequate drainage holes but some pots only have one at the base and may be blocked


How to Prevent Waterlogged Pot Plants & Soil

  • A waterlogged soil is not a healthy environment for plants to live. Much like we would not be comfortable living under water all the time.  We need to come up for air and the plant roots need oxygen too!
  • When plant roots sit in excess water for too long, they start to rot or decay. As the roots deteriorate, they can’t take up water, so the plant wilts. This is the same symptom of a plant that is thirsty! So you need to look for other clues to avoid accidental waterlogging in plants.
  • Be aware that water sitting in pot saucers can also cause problems. It’s also a mosquito breeding ground.
  • Self-watering pots are a great solution for keeping the soil moisture where the plants need it, while allowing excess water to get away.

How to Avoid Waterlogging in Plants Tip: Self-watering pots wick water up from the reservoir to the plant roots. This helps you control soil moisture.

Self-watering pots wick water up from the reservoir to the plant roots


Overwatering your Plants

  • Resist the urge to water your plant too often. It can actually make things worse!  Waterlogging in plants and soil compaction can create ideal conditions for diseases such as phytopthora and other fungal attacks.
  • Use a good quality potting mix that holds sufficient moisture but allows it to also drain freely. A healthy soil mix will also have lots of air pockets.
  • If the pot or container feels heavy and the plant is still wilting, excess water may not be getting away fast enough. A common cause of waterlogged pot plants!
  • If you have already drilled enough holes, you may need to actually remove your plant from the pot to save it.  Spread out a number of sheets of newspaper in a tray.  Lay the pot on its side and gently slide out the plant’s root ball.


Lay waterlogged potted plants gently on their side

Lay waterlogged potted plants gently on their side before removing the plant for re-potting


  • Allow the root ball to dry on the newspapers for about 12 hours. Using clean sharp scissors or secateurs, trim off any dark-coloured (brown rather than white) or slimy roots.  When you are finished, re-pot the plant in a clean container with some fresh potting mix as already outlined.
  • Whilst most books and websites on container gardening recommend the addition of coarse material such gravel, sand, pebbles, pottery shards or polystyrene pieces to the bottom of pots to improve drainage, scientific research studies have consistently demonstrated quite the opposite is true.  According to one scientist, Dr Chalker-Scott, Extension Horticulturalist and Associate Professor at the Washington State University:


“Nearly 100 years ago, soil scientists demonstrated that water does not move easily from layers of finer textured materials to layers of more coarse textured.  Since then, similar studies have produced the same results.  The coarser the underlying material, the more difficult it is for the water to move across the interface.  Gravitational water will not move from a fine soil texture into a coarser material until the finer soil is saturated.  Since the stated goal for using coarse material in the bottoms of containers is to “keep soil from getting water logged,” it is ironic that adding this material will induce the very state it is intended to prevent.”


Fertilising after Waterlogging in Plants

  • Pot plants that have been inundated with water will also have likely leached out much of the plant food or fertiliser that was in the pot previously.  You will need to replace this food source with some more organic fertiliser to ensure your plant has the energy it needs to regain its health. Top up with mulch too.
  • If you notice discoloured or yellowing leaves, this is often a sign your plant is crying out to be fed. This is because it is missing essential minerals in its ‘diet!’  A slow release, powdered or pelleted organic fertiliser and compost can help restore the nutrients.
  • If the ‘plant patient’ is really suffering, a foliar spray (on both the top and underside of the leaves early in the morning with kelp/seaweed), will give it a quick ‘pick me up.’  Use a spray bottle for this. See Frugal Gardening: 5 Thrifty Recycling Ideas on how to get one for free.


Waterlogged Pot Plants: Discoloured leaves can indicate a mineral deficiency in your plants.

Discoloured leaves can indicate a mineral deficiency in your plants.


  • To minimise future waterlogging from heavy rains and storms, consider moving your pots to a  more protected position. Under an eave on a veranda or balcony is ideal.


Pot plants on a stand, protected from too much rain

If your pot plants are exposed to the weather, consider moving them to a more sheltered position


  • Add a layer of mulch to the top of your pots. This also stops valuable potting mix from splashing out of the pot and provides a buffer between the soil and the water.


There are a wide variety of mulches you can add to pots to buffer the effects of the weather

There are a wide variety of mulches you can add to pots to buffer the effects of the weather.


Work with Nature!

  • If you live in a high rainfall area and your plants are constantly getting swamped, consider working with nature – not fighting it!  Start again with water loving plants that thrive in wet conditions. You’ll have less work to do in the garden as a result and have more success.
  • If your garden has escaped being flood, storm or rain affected, now may be the time to take a few cuttings and share them around with neighbours, schools or community gardens that suffered damage.  No doubt they will be warmly appreciated.
  • Starting over from scratch can be very disheartening, but when seeds are replanted and others offer help, the task doesn’t seem as daunting.
  • Gardens have an amazing capacity to heal the spirit. They provide a haven, hope and watching nature regrow and renew itself, often helps humans do the same.  It is well summed up in this quote:

“The greatest gift of the garden is the restoration of the five senses.” – Hanna Rion

For more problem solving tips, find out how to re-use old potting mix rather than throwing it away or make your own with my easy DIY potting mix recipe.

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© Copyright Anne Gibson, The Micro Gardener 2016. All rights reserved.