How to manage nutrients after waterlogging

Waterlogging affects nutrients in soils, and reduces the ability of plant roots to take up nutrients. Root functions require oxygen. Root growth and access to soil nutrients are restricted in waterlogged soils.

Soil test before planting the next crop to check nutrient status. Nitrogen (N), potassium (K), sulphur (S) and boron (B) can become deficient. Manganese (Mn) toxicity can be induced.


Leaching occurs when water moving through the soil takes mobile nutrients with it. Following a wet year, mobile nutrients like N, S and B are likely to have leached. K can leach from sandy soils but is less mobile in clay soils. Deep soil testing reveals if sufficient nutrients remain within the root zone.

Nitrogen and microbes

Waterlogged soils can lose N via changes in microbial activity.  In waterlogged soils, nitrifiers are less active and denitrifiers become more active. This means less nitrate-N gets mineralised. At the same time, nitrate-N already in the soil gets converted to nitrous oxide (N2O) or dinitrogen (N2). These gases are not held in the soil and move into the atmosphere. The outcome is less nitrate-N available to plants, and an overall loss of N from the soil.

Applying N fertiliser to replace lost N needs to wait until the soil has drained. Don’t apply N to waterlogged soils because:

  • Significant amounts of applied N may be lost through volatilisation.*
  • Applied N converted to nitrate may denitrify and be lost to the atmosphere while the soil remains waterlogged.
  • Applied N might be lost with runoff or via leaching if it rains again.

* The conversion (hydrolysis) of urea to ammonium and ammonia can induce highly alkaline pH in wet soils, promoting volatilisation).

Manganese toxicity

In waterlogged soils, anaerobic microbes convert inert manganese (Mn3+) oxides to plant-available Mn2+.This form of Mn is rapidly taken up by plants. Canola is one of the most susceptible crops to problems from too much plant-available Mn. Legumes are sometimes affected. Symptoms include yellow chlorosis and small brown spots.

Mild manganese toxicity often resolves as soils dry. Liming will help if low pH is contributing to Mn toxicity.


More information

What can you do with waterlogged paddocks

Three reasons why topdressing Nitrogen can fail

How to confidently diagnose a crop nutrient disorder

Denitrification and managing nitrogen loss risk – key factors affecting loss

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