Original Agriculture Victoria Note Number: AG1436. Published: February 2011. Reviewed: May 2013.

Flooding of orchards can occur as a result of rainfall or from flooding from rivers or streams. If the soil remains waterlogged (saturated) for extended periods, plant health will be affected in a number of ways.

What should I do?

The best strategy is to drain or pump water from the orchard within 48 hours. Where possible a spoon drain dug in the centre of the traffic line will help surface drainage.

Where flooding is landlocked, a sump can be dug to assist pumping. Over time the water will also be removed by transpiration by weeds and soil evaporation largely assisted by wind movement. A permanent sward in the orchard will facilitate the drying process.

Where tree roots have been damaged by waterlogging (saturated soil) and root rots (Phytophthora Spp.), irrigation should be scheduled carefully to allow for the reduced root uptake and avoid water stress in the trees. Careful irrigation scheduling will assist in leaching salts away from the tree roots.

Waterlogged soils

The full impact of inundation or waterlogging will not be apparent for some time after the event so ongoing monitoring is important to manage tree health and identify issues. Waterlogging may continue particularly in clay soils and duplex soils with a shallow clay layer below the surface soil. Digging a hole or installing a test well can help monitor the water table depth and hence the degree of waterlogging.

If the soil remains waterlogged for extended periods plant health will suffer because the air between soil particles is displaced by water and a lack of oxygen in the soil will result in root and eventually plant death. Symptoms of waterlogging stress include wilting and chlorosis of leaves due to lack of nitrogen and shoot dieback. There is also potential to affect growth in the following season. Flooding may also cause leaching of nutrients, loss of mulch material or slumping (slaking and dispersion) of the soil and will need careful management. Shallow, stagnant water can heat up quickly in hot weather and kill tree roots so it is important to remove excess water quickly.

Most soils, especially those with a high clay content, become compacted and slump after heavy rainfall and flooding. Flood waters can also deposit a fine clay layer or crust on top of the soil that prevents oxygen and water penetration of the soil.

Salinity may be a consequence of waterlogging because salts (e.g sodium chloride) in the subsoil, moved into surface soils by flooding and rising water tables, become highly concentrated and damage tree roots as the soil dries. When root function is impaired by a lack of oxygen the plant has difficulty keeping sodium and chloride out of the roots and the trees accumulate more salt than normal. This will be indicated by the leaves showing signs of marginal necrosis or salt burn.

Water logging tolerance of stonefruit and almonds

Cherry, apricot, and peach trees are very sensitive to water logging, where plum trees are generally less sensitive. Almond and apricot trees are amongst the most sensitive of all deciduous trees to soil waterlogging and should be planted in well-drained sandy soils.
Peach rootstocks may start to die after only two to five days of flooding if soil temperatures are high. This can vary depending on the rootstock. For example, Nemaguard rootstocks, a common industry rootstock used in Australia, are considered intolerant of flooded soil conditions, whereas Cadaman, Krymsk1 and Krymsk86 rootstocks are more tolerant to wet conditions.

Surface drainage

In new plantings, or where feasible in existing orchards, mounding of the soil along the treeline for improved surface drainage should be carried out. A road grader, designed for this task, is preferred over an orchard tractor to ensure accurate layout and minimal damage to soil structure. Connecting drains to carry drainage water away from the orchard on a suitable grade are just as important. Best practice management for surface drainage involves the use of laser guided machinery or alternatively a survey with an optical level to establish an accurate grade in the surface drains. Poor drainage is further exacerbated by wheel ruts created by tractors and implements operating in the wet soil and should be avoided. Specific areas that remain waterlogged for long periods, need to be identified for remedial action in the future, e.g. by installing drainage.

Ponding of water in the orchard

Ponding of water in the orchard caused by poor drainage

road grader

A road grader accurately and efficiently improves the orchard layout

Soil management

It is important not to drive in the orchard while the soil is very wet because compaction of the soil and wheel ruts will result. There may be issues with hard setting of the soil as it dries but cultivation when the soil is too wet should also be avoided. If there is a heavy clay subsoil, to inhibit drainage and result in a perched water table, treat the area by applying gypsum (rate determined by a soil test) to the treeline. If the soil has set hard, once it is dry (at field capacity) a "one-off" light cultivation may be desirable to break up the compaction to allow water and oxygen to penetrate. However, care should be taken for cultivation has the potential to pulverise the soil and further damage soil structure.

If sections of the orchard require re-planting a soil test beforehand is advisable so soil amendments, e.g. gypsum and lime can be added. An organic mulch e.g. straw spread on the treeline will reduce crusting plus improve water penetration, aeration and drainage of the soil profile. Farmyard manure and organic mulches applied to the vine line can encourage beneficial fungi antagonistic to Phytophthora root rots.

In autumn, re-sowing the cover crop or permanent sward damaged by the flood, will assist in replacing organic matter that may have been lost in the flood as well as improve soil structure and aeration A cereal crop such as oats or a medic are suitable cover crops. Cereal crops will be easier to establish and will provide straw for mulching.

Root Rots

Irrigation scheduling must be done carefully to avoid saturated soil conditions that accelerate the spread of Phytophthora Root Rots. Root disorders need to be identified and root diseases distinguished from environmental damage to roots caused by waterlogging and poor establishment at planting. The loss of a significant proportion of roots and the invasion of the vascular system of the tree by the pathogen may result in defoliation and ultimate death of the tree through restricted uptake of water. Soil diseases are difficult to identify so suspected soil and root samples should be taken for disease identification which can be carried out by the Crop Health Service (03 9032 7515). For more information, see the Information Note, Phytophthora Root and Trunk Rot of Pome and Stone Fruit.

Improvements in soil structure by the addition of gypsum and organic matter to increase air-filled porosity, infiltration and drainage of water will also assist in the management of root rots. A combination of better soil structure, careful scheduling of irrigation and chemical control is recommended.

A monitoring program should be based around identifying the areas infected by the disease followed by a qualified and quantitative assessment of chemical control measures. Specific information on chemicals, formulation, registration, application rates and withholding periods is advice that needs to be provided by an authorised person and therefore should be sourced from chemical suppliers.


Heavy rainfall and flooding can cause nutritional deficiencies due to leaching of nitrogen, potassium and boron out of the root zone. Silting may cause de-nitrification of the soil by bacteria as a result of less oxygen being present in the soil and is significant when the soil has been waterlogged for 36 hours or more.

Nutrients such as nitrogen, phosphorous and calcium can also have their uptake inhibited under waterlogged conditions. Fertiliser applications should be adjusted to make up for any shortfalls, however adjust rates with caution as over application will also need to be avoided. It will be essential to undertake petiole/leaf analysis the following season and tailor fertiliser applications to the tree needs.


Apart from root rot issues, many fruit and leaf diseases are more active in wet, humid conditions. Where water is laying or soils are waterlogged, humidity will be higher adding to disease pressure and this should be taken into account when considering disease control programs.

It will be important to maintain tree health and control diseases in order to maintain leaf cover and maximise laying down of nutrients for the following season. Trees should be monitored closely for increased presence of fungal and bacterial diseases. A complete list of pesticides with registrations is available from the APVMA website.

Contact/Services available

Correct diagnosis is essential for effective pest and disease control. A commercial diagnostic service is available. For further information, phone Crop Health Services on (03) 9032 7515 or fax (03) 9032 7604.

AgriBio Specimen Reception
Main Loading Dock
5 Ring Road
La Trobe University
Bundoora VIC 3083



Responses of fruit crops to flooding, Schaffer et al 1992
Rootstock performance in stonefruit, Mark O’Connell Agriculture Victoria, 2020

This Agriculture Note has been prepared by Agriculture Victoria in February 2011.

The advice provided in this publication is intended as a source of information only. Always read the label before using any of the products mentioned. The State of Victoria and its employees do not guarantee that the publication is without flaw of any kind or is wholly appropriate for your particular purposes and therefore disclaims all liability for any error, loss or other consequence which may arise from you relying on any information in this publication

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