Soaks are seeping across the Mallee – what can be done about it?

Author: | Date: 11 Feb 2020

Take home messages

  • Seeps are rapidly growing as a result of modern farming systems, landscape and seasonal factors.
  • Early identification and action are imperative and can be assisted through satellite NDVI imaging.
  • Specific management strategies must be applied within recharge, discharge and interception zones to prevent the initial problem of unused freshwater developing into large unproductive saline scalds.


Seeps resulting from localised, perched water tables have become a degradation issue across the cropping zones of SA and Victoria over the last 20 years and have rapidly increased over the last decade. This was highlighted in a recent survey involving 80 landholders across the Mallee region (McDonough, C. 2017). Their emergence is due to a combination of landscape, seasonal and farming system factors, leading to the waterlogging, scalding and salinisation of productive cropping ground in swales, a reduction in paddock efficiencies, and increased machinery risks.

Diagram depicting the formation of Mallee dune seeps near Karoonda, South Australia.

Figure 1. The formation of Mallee dune seeps near Karoonda, SA, (adapted from Hall, J. (2017) pp. 31).

Modern farming improvements toward no-till and continuous cropping have led to near total control of the previously dominant deep-rooted/perennial summer weeds like skeleton weed. This is leading to a greater storage of summer rainfall, which passes through the sandy rises with very low water-holding capacity. Figure 1 demonstrates the resulting formation of perched water tables above areas of impervious clay layers, (such as Blanchetown Clays). Water moves laterally toward lower-lying areas of the paddock and reaches the soil surface where the clay comes close to the surface in mid-slopes, or at the base of swales. This results in waterlogging, capillary rise, evaporation and salinisation over time at the discharge site.

Seeps generally begin as areas inundated with excess fresh water, which will lead to permanent salinisation and land degradation usually within three to four years if no remediation occurs. However, some perched water tables emerge and become quite saline over a longer period of six to ten years. These have only recently displayed surface expression due to changes in agronomic practices during recent years e.g. summer weed management. The key to managing seeps is to identify the problem early, assess and apply appropriate management into the three key zones; recharge, intercept and discharge areas (see Figure 1):

  • recharge zones – where most of the excess water is entering the system
  • discharge zones – where the problems are developing at the soil surface (often in mid-slope or lower-lying areas)

potential interception zones – where higher water use strategies can utilise the excess water before it reaches the discharge zones.

This paper presents findings and strategies resulting from several seep monitoring projects conducted over the last five years involving seven sites over six farms. Each site involves the use of moisture probes, piezometers and rain gauges with continuous data loggers. In addition, detailed landscape soil testing and treatment monitoring was used to more accurately assess the dynamics of the catchments, impacts of rainfall events and various management strategies. Growers were directly involved in developing and applying practical strategies to remediate the problems.

This research addresses many important understandings, outcomes and strategies for growers and advisors in dealing with this growing, land-degradation issue. Further results and new approaches will continue to develop as part of a collaborative project between Mallee Sustainable Farming (MSF), the GRDC, the Australian Government’s National Landcare Program — Smart Farming Initiative and the SA Murray Darling Basin NRM Board.

Results and discussion

Identifying the problem

There are several key indicators that a seep area may be forming. Initially the crop below a sandy rise, or lower in a catchment area, may produce substantially higher growth or yield, due to accessing the extra moisture from the beginnings of a perched, fresh-water table. This is often more evident through drought years. It is not uncommon to find a distinct saturated layer of soil within the top 1m (sometimes slightly deeper) where this is happening. Ideally, this is the time to commence remedial action, well before it grows into a degraded soil area.

Large crop growth or yield in the developing seep is usually succeeded by ryegrass becoming thick and dominant through a cereal or pasture phase. Ryegrass tends to be more tolerant and responsive to seep conditions, persisting well into summer with a large seed set which is likely to contain a high percentage of hard seed.

As the seep areas grow it is common to find tractors suddenly sinking to their axels and causing major operational disruptions around these sites. The perched water table gets closer to the surface and bare, scalded areas will start to emerge due to anaerobic soil conditions that are detrimental to most plant growth. Depending on rainfall and landscape factors, surface ponding may occur for periods after rainfall events. This is a critical phase as, particularly over the heat of summer, as bare soil conditions will lead to capillary rise of moisture, evaporation and accumulation of salt at the surface to toxic levels for crop growth.

In recent years it has become evident that whilst wet years (such as 2010/11 and 2016) have resulted in seeps developing in these catchments, it is the drier years, with less plant growth and longer periods of heat and evaporation, that greatly exacerbate the accumulation of surface salt.

Normalised Difference Vegetation Index (NDVI) mappinghas grown in prominence in recent years as a way of monitoring crop and pasture growth in precision agricultural management.  NDVI images can be obtained from both drones and satellites, and essentially indicate areas of good or poor vegetative growth through spatial colour images. In 2017 a NR SAMDB project (McDonough, C. 2018a) found that strategic use of NDVI imaging can be used to identify both the formation of Mallee seep areas, as well as the potential threat to surrounding areas becoming degraded.

Consultants and growers are using numerous NDVI satellite use programs such as DataFarming and Decipher to identify areas of poor crop growth. The satellite images are convenient, free to access for the levels required, and are becoming a vital tool for seep management. A guide to the use of an NDVI mapping program is available on the MSF Mallee Seeps Website.

The key principle to reading NDVI images is to look at cloud free images over multiple dates through October to December. Soils remain wetter-for-longer in perched water table areas, resulting in extended periods of plant growth in spring. This is particularly evident in annual species, which show up clearly in contrast with normal crop areas that have already matured. Sites can then be analysed to assess the impact of seeps on the landscape.

The main advantage of NDVI imagery is that it shows the extent to which bare seep areas are likely to spread if nothing is done. In many cases it has been revealed that an easily visible bare patch of 0.2ha has the potential to quickly impact 5ha or more, due to a clear indication of excessive water and growth in the surrounding area. This provides a strong incentive for growers to take immediate remedial action, rather than observing degradation develop over time.

Figure 2. NDVI Map from the sixteenth of October 2017 showing large areas under threat from seep degradation

Figure 2. Normalised difference vegetation index (NDVI) map 16 October 2017 showing large areas under threat from seep degradation (dark (blue) shading).

Viewing images throughout the growing season may also identify areas of poor crop growth which may contribute directly to recharge after rainfall. These areas can then be targeted for specific management options. Ground truthing of images, along with local grower knowledge, is vital in ensuring an accurate mapping of potential seep areas and identification of other unrelated factors influencing growth. For example, frost events can lead to crops reshooting late in the season and staying greener, for longer, in low lying areas. Also, summer crops or uncontrolled summer weeds may also present as similar NDVI image colours as seeps, as can trees or other perennial vegetation. Cloud cover and cloud shadows can cause distortions and misinterpretations, which is why it is important to view multiple images over a timeframe.

Management zone strategies

Once seeps and surrounding areas at risk have been identified, it is important to implement management strategies as soon as possible. Ideally, these should be designed to best fit within the grower’s systems, with minimal disturbance to normal paddock activities. Some strategies may even lead to higher paddock productivity.  However, some ‘less convenient’ changes may be necessary to protect a greater area of productive land heading towards total degradation and problems.

It is generally a combination of management strategies targeted in each of the recharge, discharge and interception zones is required to stop the spread of seeps and possibly bring the damaged area back into profitable production.

Recharge zone

Site monitoring shows that deep sands (often non-wetting) are the main source of excessive recharge water entering the system. Deep sands have very low water holding capacity and soil fertility and often suffer from compaction that restricts rooting depth. This means that even relatively small rainfall events can quickly pass through the root zones to contribute to the perched water table below.

Figure 3 illustrates the rises in water table at the mid-slope piezometer site between November 2015 and May 2018 at Wynarka, including the wet spring of 2016. The perched water table at this site is below the crop root zone, so any level rise is a direct impact of rainfall contributing recharge from the 60m of sandhill slope above the piezometer.  Any fall in levels is likely due to discharge, evaporation or transpiration of the water lower in the system (particularly in the hotter summer periods), or in some cases, a bulge of water moving down the slope after a larger rainfall event. It reveals that a 40mm rainfall event raised the mid-slope water table by over 40cm. Smaller events of 12mm and 15mm during the 2017 growing season led to rises of 15-20cm. Even a sudden 7mm rainfall event in December 2016 caused a rise in water table of 10-15cm.

Figure 3. Graph depicting how the Midslope (RO2 piezometer) water table rises after specific rainfall events from November 2015 to May 2018

Figure 3. Midslope (RO2 piezometer) water table rises after specific rainfall events (November 2015 to May 2018).

The key principles for managing the recharge areas is firstly to break any soil compaction, effectively increasing the plant root zone from around 20cm depth to down to 150cm (as observed at one site). This allows crops to dry out new rootzones to wilting point with benefits to crop growth and yield, while also creating a larger ‘bucket’ to fill before it starts contributing to recharge.

Soil amelioration that incorporates clay or nutritious forms of organic matter such as manures into the top 40cm often improves soil water holding capacity within this rooting zone. This was clearly evident at a Karoonda seep monitoring site, where spading in chicken manure more than doubled crop yield over a four-year period. Soil moisture probes showed excellent soil water retention within the 40cm spading depth which was utilised by the crop. This was in direct contrast to the untreated control plot which produced low yields, very little soil moisture used by crops below 30cm depth, and numerous rainfall events contributing to recharge (McDonough 2018b).

Any practical, effective and safe method of achieving soil amelioration through deep ripping, delving, spading, clay-spreading or manure/organic matter/nutrition incorporation will be beneficial in increasing crop water extraction and remediation of sandy recharge zones. Current research is developing more options for growers in this pursuit.

Some growers have decided their deep sands aren’t worth cropping and have chosen to establish permanent perennial, deep rooted pasture options such as lucerne or veldt grass. This becomes a viable option for growers with livestock in their systems, providing valuable feed options at critical times. However, care is needed in establishing pastures into adequate soil cover within favourable seasons to reduce the risk of wind erosion. In 2019, a grower at one site chemically fallowed their sandhill until sowing lucerne in August. This avoided a dry period from May to June which coincided with high winds and achieved an excellent stand as the soil warmed up in spring.

Discharge zones

The main principle for discharge zones is to try and maintain living soil cover all year around if possible. This greatly reduces capillary rise of moisture to the surface, and evaporation leading to surface salt accumulation, due to plant roots drawing moisture from deeper in the profile. Bare soil over the summer months and dry seasons, will lead to a rapid deterioration of soils into unproductive, saline scalds. The strategies to best manage this will depend on the development stage of the seep.

When a perched water table is in its early stages when crop yields are often increased, it is important to try and maintain cropping through these areas, without getting machinery bogged. As soon as practical after harvest, sow a summer crop in these zones to dry them out. A mixture of sorghum and millet has been successfully used over three seasons by growers near Mannum. With very little summer rainfall in this period the summer crops grew well where excess moisture was accumulating, but soon died out in the dry sandy soils surrounding the seeps. Summer crops are either cut for hay or harvested prior to seeding the winter crop.

Despite the growth of the summer crop in the discharge area, this did not lead to any yield loss in the following winter crop, as the soil continued to be recharged from higher parts of the landscape. While summer crops do not address the problem at its source, they greatly reduce soil degradation, with minimal impact on the grower within their normal cropping program. This method will only be effective long term if management strategies are also employed to address the excess water emanating from the recharge and interception zones.

For an established scald with high surface salinity or waterlogging affecting crop growth, a perennial salt tolerant pasture such as puccinellia or tall wheat grass should be considered. Ideally these can be sown with airseeders, but where heavy machinery cannot access the seep site, salt tolerant pastures can be established by spreading seed through a rabbit baitlayer and dragging harrows behind a quadbike. It has been reported that puccinellia is suitable for areas with moderately-high to very-high salinity (8 to >32dS/m), and tall wheat grass tolerates low to moderate levels (0-8dS/m, Liddicoat and McFarlane, 2007).

Current demonstrations resulted in good establishment at a variety of salinity levels, including excellent puccinellia establishment on a crystalline salt-covered scald at Wynarka. In some cases, tall wheat grass has established later in the season where puccinellia has not grown, even though they were sown together in the same seed mixture. The salt tolerant annual legume variety Messina has also been tried, but generally struggled on bare scalded sites. In addition, saltbush has been grown and grazed successfully in some seep areas, however it has not survived well in areas with periodic water inundation.

The successful establishment of pastures appears to depend on seasonal factors and more specific soil parameters not considered in previous work at more saline sites. Even slight rises in surface soil levels (i.e. raised beds????) or additions of organic matter have improved survival. Saline seeps are extremely alkaline with soil pH approaching 11 in many cases, which is toxic to most plant growth. This also needs to be considered when selecting salt tolerant species.

The MSF seeps project aims to gain a better understanding of the various mechanisms leading to saline seeps and better management decisions, by measuring soil parameters at different times throughout the seasons across different management practices. Initial success has been shown using a front-end loader to introduce a 10cm layer of sand, straw and manure to bare scalds, which improved establishment of salt tolerant grasses, and even a cereal crop at one site. These sites are being monitored over coming seasons to see if they will deteriorate over time or continue towards greater improvements.

In seep areas that have salt-scalded centres too toxic for crop growth, it is still important to employ these strategies on the less toxic edges to restrict the spread of these scalds.

Interception zone

Below the recharge zone there is a lateral subsoil flow of excess water above the impervious clay layers before it hits the discharge area (Figure 1). This area provides an opportunity to intercept and use this water before it causes problems lower in the landscape. At all monitoring sites the most successful strategy applied within this interception zone has been the strategic establishment of lucerne, with roots that penetrate deep into the perched water table to produce hay or pasture throughout the year. Lucerne effectively exploits large summer rainfall events that normally cause water recharge and is a versatile option that is familiar to growers. Figure 4 shows that each major rainfall event in the lucerne site area was quickly utilised with no evidence of recharge. This contrasts with the continuously cropped side which regularly had 60-70mm more water in the top 100cm soil passing beyond the rootzone. In the extremely wet season of 2016, the midslope lucerne was the only site to experience a reduction in the water table.

Growers are now targeting strips of lucerne (often 30-50m wide) above seep areas to intercept the lateral water flows and benefit from the productive fodder production. Even growers without livestock can boost their profits by selling lucerne hay produced off these areas. Crops can be sown through these lucerne strips, so establishing lucerne in the same direction as cereal sowing may be worthwhile, even if it takes more initial effort. While encompassing these lucerne strips within cropping paddocks may require some compromises, it is still better than losing expanding areas of highly productive land to seeps.

Figure 4. Two line graph Comparisons of top 1 metre soil moisture levels in lucerne and cereal treatment areas from July 2015 to May 2018

Figure 4. Comparisons of top 1m soil moisture levels in lucerne and cereal treatment areas (July 2015 to May 2018).

While growers may not wish to plant trees in the middle of cropping paddocks, these may worth considering, particularly where a fence line or laneway already exists. If planting trees close to seeps, it may be worth testing water quality to assess the level of salt tolerance required. Tree guards to protect seedlings from vermin and some early watering to ensure summer survival on deeper non-wetting sandy soils are recommended.

Innovative strategies

The MSF seeps project is currently conducting several trials and demonstrations of innovative management options, including the use of a subsoil extruder to apply organic amendments on deep sands above a seep at Alawoona. This machine applies a manure slurry behind deep ripping tines with minimal increases in erosion risk, unlike spading. Initial improvements in crop production and water use are promising.

Other trials are assessing other subsoil amelioration techniques, alternative pasture species and use of long season varieties to extend the growth period. One site is assessing the practicality of an in-ground sump and pump, just above a seep scald area, to extract water for spraying, livestock or liquid fertiliser application, however, poor water quality is presenting some challenges.


Localised seeps are a growing land degradation issue across cropping zones of southern Australia, due to a combination of landscape and seasonal factors as well as changes associated with modern farming systems. Early detection and treatment is vital to avoid rapid expansion of seep areas.

Various projects in the SA Murray Mallee have identified a number of strategies that provide practical options for growers to apply into the three critical areas of recharge, discharge and intercept zones. New technologies such as NDVI satellite imaging are providing important resources for early detection of developing seeps and the potential threat to grower’s paddocks if left unmanaged. Ongoing work is refining these strategies through the MSF Mallee Seeps project to improve water use efficiencies and remediation of these issues.


The current research is a collaborative project between Mallee Sustainable Farming, the GRDC, the Australian Government’s National Landcare Program — Smart Farming Initiative and the South Australian Murray Darling Basin Natural Resource Management Board. The research undertaken as part of this project is made possible by the significant contributions of growers through both trial cooperation and the support of the GRDC, the author would like to thank them for their continued support.


Hall, J. (2017) Mallee dune seepage in the SA Murray Mallee - summary report. Natural Resources SA Murray-Darling Basin, (Deptartment of Environment, Water & Natural Resources, Government of SA: Murray Bridge).

Liddicoat, C. and McFarlane, J. (2007) Saltland Pastures for South Australia. (Department of Water, Land and Biodiversity Conservation: South Australia).

McDonough, C. (2017) Mallee seeps farmer survey 2017. In, ‘Report for Mallee Sustainable Farming’.

McDonough, C. (2018a) The Use of Normalised Difference Vegetation Index (NDVI) to Manage Seeps. In, ‘Martins report, Karoonda’. SA Murray-Darling Basin, Natural Resources Management Board.

McDonough, C. (2018b) Monitoring Mallee seeps summary, project 1569C for the South Australian Murray-Darling Basin, Natural Resources Management Board.

Contact details

Chris McDonough
Insight Extension for Agriculture
0408 085 393

GRDC Project code: 9176969