Waterlogging – the science

Page last updated: Tuesday, 18 May 2021 - 4:08pm

Please note: This content may be out of date and is currently under review.

Waterlogging is a common problem in the agricultural soils of south-west Western Australia in the wetter months of winter.

Almost two-thirds of the agricultural land in the south-west region has a duplex soil profile with sandy loam surface soils over sandy clay subsoils. These soils are susceptible to waterlogging when the amount of rainfall exceeds the ability of the soil to drain away soil moisture. This susceptibility is increased by the strong texture contrast between sandy topsoils and clay subsoils: infiltration is higher through the topsoil than in the subsoil.

What is waterlogging?

Waterlogging is excess water in the root zone accompanied by anaerobic conditions. The excess water inhibits gaseous exchange with the atmosphere, and biological activity uses up available oxygen in the soil air and water – also called anaerobiosis, anoxia or oxygen deficiency.

Soils don’t have to be saturated (waterlogged) for gas exchange to be inhibited.

These conditions affect agricultural plants in several ways:

  • nutrient deficiencies or toxicities
  • root death
  • reduced growth or death of the plant.

Waterlogging that causes death of deeper roots in winter can lead to droughting of plants in spring and early senescence of annual crops and pastures in the Mediterranean climate of south-west of Western Australia.

Measuring waterlogging

Measure waterlogging in the plant's root zone with shallow wells. Water that is perched on subsoil clays progressively saturates the topsoil from below and inhibits the exchange of oxygen, carbon dioxide and ethylene with the atmos­phere.

To install the wells:

  • Drill holes just into the clay subsoil, or to 70cm if no clay had been encountered by that depth.
  • If the well is to be used for the season, fit slotted PVC pipe to the depth of the hole and leave a small amount above ground to help prevent surface water entering.
  • Pack coarse sand around the slotted PVC pipe, so that water perched on the clay subsoil can enter through the slots. Use clay from the hole to form a seal around the neck of the PVC pipe to prevent surface water entering.

Severity of waterlogging

Waterlogging throughout the year and at different soil  depths can be integrated by the Sum of Excess Water that occurs each day in the primary root zone of the top 30cm soil layer (SEW30) (Setter & Waters 2003). SEW30 is the sum of all daily values (in centimetres [cm]) by which watertables are closer than 30cm to the soil surface (in units of centimetre days [cm.days]). For example: 10 days rising to 10cm below the surface (20cm above the 30cm depth measured) is 10 x 20 = 200cm.days. See Table 1 for waterlogging classes.

Table 1 Waterlogging classes using the SEW30 index
Waterlogging class
(in terms of drainage)
SEW30 index
(cm.days in an average growing season)
Well drained <30
Moderately well drained 30–100
Moderately drained 100–250
Imperfectly drained 250–500
Moderately poorly drained 500–1200
Poorly drained 1200–2500
Very poorly drained >2500

Table 1 is derived from Bulletin 4343 Soil Guide: a handbook for understanding and managing agricultural soils (Note: this is a large PDF download).

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How waterlogging affects plant growth

The SEW30 index is a guide to the potential effect on plant growth, but there are many factors that influence the interaction between waterlogging and plant growth. Conditions which might substantially interact with SEW30 to affect growth include:

  • salinity of the soil water
  • nutrient levels in the soil water
  • temperature
  • frequency of waterlogging
  • flooding
  • stage of development.

Transient toxicities

Waterlogging lowers oxygen levels in the root zone, which reduces plant growth. Waterlogging increases the reduction potential of the soil and changes the chemical equilibrium of many elements which then enter the soil-water solution in their ionic forms.

Depending on soil type, this change in chemical equilibrium can include transient toxicities of some soil nutrients that are normally safe when soil is freely drained. Examples of these are iron and manganese compounds which can be converted into free ions when reduction potential is high.

The reduction potential can take several days or longer to return to normal levels after the waterlogged soil has drained. Regular rainfall can cause repeated waterlogging and drainage cycles, and the soil can have high reduction potential for long periods.

Clay that is repeatedly waterlogged for long periods often appears blue-grey, and may have a swampy smell.

Damage to germination, seedlings and rapidly growing plants

Waterlogging or inundation of the seedbed affects germinating seeds and young seedlings more than mature plants. Earlier-sown crops that have emerged and are well established can tolerate waterlogging more than plants that are emerging during waterlogged conditions.

Plants are more susceptible to waterlogging:

  • in the cold, wet conditions of winter in south-west WA
  • when seedlings have reduced carbohydrate production needed for healthy roots (occurs with low leaf area and low solar energy)
  • when they are growing rapidly and nutrient demands are increased. However, in WA, this rapid growth happens when the weather warms up and rainfall is decreasing in spring which means that waterlogging yield reductions are less common at this time of year.

Waterlogging causes root-tip death within days. Loss of root tips limits the uptake of nutrients (particularly nitrogen) and water after waterlogging. As a result, plants that have been waterlogged ripen early and grain is often pinched.

Nitrogen loss and lowered plant uptake of nitrogen

Nitrogen is lost from waterlogged soils by leaching and denitrification – the process where nitrogen is converted to gaseous oxides of nitrogen. These losses, together with the lowered ability of plants to absorb nutrients from waterlogged soil, cause the older leaves to yellow. Waterlogging also directly reduces nitrogen fixation by the nodules of legume crops and pastures.

Adding nitrogen soon after waterlogging recedes can reduce the impact of waterlogging by making more nitrogen available to the crop at the time it needs it. Correct timing of nitrogen application on waterlogged crops can significantly increase yields and reduce nitrogen fertiliser costs.

Nitrogen fertiliser can be added as granules or liquid:

  • Liquid fertilisers can supply nitrogen directly to the leaves and crop canopy to replace nitrogen normally supplied from the soil, and can therefore be applied at any time.
  • Granular fertilisers are more effective if applied immediately after waterlogging has gone.

Note: Severely waterlogged crops may have their yield potential lowered to such an extent that adding nitrogen will not be profitable. We recommend growers seek professional advice in that situation.

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Waterlogging can lead to soil structure decline

Waterlogged soils tend to collapse quickly through dispersion of clay particles. This is especially the case in soils with high sodium:calcium ratios; these soils are often called dispersive or sodic soils.

Waterlogged, non-dispersive soils can also lose soil structure by:

  • collapsing under their own weight in the absence of additional strength generated by the soil moisture suction of unsaturated soil
  • disturbance by machinery or livestock when saturated at the surface.

Driving across waterlogged soils will damage soil structure. Minimise the area of damage by using a tramline or controlled traffic farming system, which also improves trafficability during seeding, fertilising and spraying operations on waterlogged soils. The tramlines themselves are susceptible to water erosion, and we recommend surface water management structures to minimise the risk of damage.

For more information

The waterlogging landing page has links to other relevant pages.