Managing contaminated livestock water

How to manage contaminated stock water supplies after a flood

Farm dams and channels can become contaminated after a flooding event. This may lead to limited water supplies for stock and dairy sheds.

Pollutants such as manure, vegetation, chemicals, and animal carcasses can affect flood water. Decaying plants and animals in the water also increase the risk of diseases such as E. coli and botulism. Water quality issues can develop over time if water flow stops in areas with organic material and manure. This can lead to pathogen growth and potential blue-green algae concerns in the water.

Managing water quality after a flood is complex and each situation is unique.

Safety around farm dams and dairy effluent systems

Farm safety and accident prevention should be the highest priority on-farm, ensuring the property is as safe as possible for:

  • workers
  • children
  • visitors
  • livestock and
  • pets.

Before assessing the quality of livestock water supplies, make sure it is safe to access the area. Some common safety tips include:

  • Always assess water systems with another person, especially if walking in or around dams, to reduce the risk of drowning.
  • If you cannot see the edge of the dam when taking a water sample, wait until flood waters subside and it is safe to be near the dam.
  • Use long extension poles to collect water samples for analysis.

More information on safety, covering broader dairy operations, can be found in:

Managing contaminated stock water

Follow these steps to help you manage decisions about what to do if your stock water supply has been contaminated by floods.

1. Assess the water quality

Visually inspect water supplies for debris, dead stock, smell, and odour.

2. Is the water supply contaminated?

  • Yes. Water supply has been contaminated by flood water. Remove any floating debris and dead animals. Go to step 3
  • No. Water supply is not affected by flood water. No further action.

3. Calculate water requirements

Calculate how many days of water you have available.

  • What are your daily stock and dairy water requirements?
  • How much good quality water (if any) is available in storage?
  • Start using water saving strategies to make the limited resource go further.

Water budgeting tools and resources

4. Identify alternative water supplies

Identify alternative sources of good quality water you might have access to. This might be:

  • another dam or channel that’s not contaminated
  • groundwater that’s not contaminated
  • a neighbour’s bore or dam – check with your Water Corporation before using this supply.

If possible, empty the dam water to pasture and refill with a clean water supply, such as a channel.

The Water section on the Agriculture Victoria website provides information on water and irrigation related specifically to farming and agriculture

5. Test the water quality

If there are no alternative water sources, test the contaminated water quality. Does the test show the water quality is OK for livestock to drink?

  • Yes. No further action.
  • No. Go to step 6

6. Where no alternative water supply is available

Where water is contaminated, there’s no alternative supply on-farm and a water quality test shows it’s unsafe for livestock to drink, take one or more of these steps:

  • Treat water, using sediment removal and chlorination, if it’s safe and possible to do so
  • Purchase water from a water carrier
  • Move animals to a location where water quality isn’t affected using an agistment service.

If you are in a situation where there are no alternative stock water supplies and the main water supply is contaminated, technical water support is available from Agriculture Victoria.


  • Greg Bekker, Land Management Extension Officer, Benalla: 0417 340 236
  • Benita Kelsall, Dairy Extension Officer, Gippsland: 0429 353 649.

Where to get water tested

Use a National Association of Testing Authorities (NATA) accredited laboratory to test water quality. Before testing, contact the laboratory to get:

  • the correct sample containers
  • instructions for taking the sample and
  • information on how to return the sample to the laboratory. e.g. samples testing for E. coli or total coliform must arrive at the laboratory the same day they’re collected.

Water quality testing laboratories are located across Australia

National Association of Testing Authorities (NATA)
SGS, 20 Hotham Street, Traralgon
Phone: (03) 5172 1555

ALS Water Resources Group, Wangaratta
Phone: (03) 5722 2688

What can be tested?

After a flood it is important to test for any pathogens such as E. coli and total coliform in the water supply.

A good quality water supply can also be tested to understand the level of pathogens present. This test can provide a benchmark for the floodwater sample and help understand the actual water quality. All farms with grazing livestock will have a level of pathogens present as manure will wash into dams.

Table 1 below provides some guidelines to support interpreting the results.

Table 2 provides a list of other important water quality tests. Some of these go beyond the immediate impacts associated with floods. However, they can affect livestock. Stock water tests can also detect heavy metals, pesticides, or blue-green algae.

Table 1.  Water quality tests for contaminated stock water

Water quality detection

Understanding the results

E. coli

Levels should be less than 100/100mL for drinking water (Australian Government 2000).

Total coliform

Levels should be less than 2000/100mL for stock drinking.

Table 2.  General water quality tests to assess suitability for livestock

Water quality detection

Understanding the results

pH Value

Stock water should be between pH 6.5 – 8.5.

Total dissolved solids (TDS)

- Salinity

This is a measure of the inorganic salts in the water.

Levels above 4,000 – 7,000 mg/L TDS can impact production and see a decline in animal health and condition.


Stock can tolerate concentrations up to 1,000 mg/L.


Stock can tolerate concentrations up to 1,000 mg/L.

Nitrite as N

Concentrations exceeding 30mg/L may be hazardous to animals.

Nitrate as N

Levels should be less than 400 mg/L.


Levels over 800 mg/L can cause diarrhea and reduce milk production in dairy cows.


Levels should be less than 20 mg/L.


Levels should be less than 1000-2000 mg/L.


Trigger value is at 5mg/L.


Trigger value is 0.5 mg/L.


Levels should be less than 1 for cattle.


Levels should be less than 0.1.


Levels should be less than 0.15.


Levels should be less than 2.

Water treatment options

There are a range of ways to treat poor quality water, the Department of Primary Industries (NSW) Farm water quality and treatment document provides an overview of these.

In all cases, farmers must speak to their vet before starting any water treatment options.

Water chlorination

Chlorinating livestock water supplies is one method to kill bacterial contamination. It is only recommended under exceptional circumstances. And should occur in batches using a water tank, with no sediment.

For more information about water chlorination and treatment visit:

Note: Chlorination does not remove toxins causing botulism produced by organisms that live on rotting material.

What is the impact of blackwater?

Blackwater is water with little or no oxygen in it. It is usually dark in colour due to the breakdown of plants and other organic matter.

Contamination can cause the water to be temporarily unpalatable to livestock.

Contaminated water is not usually poisonous to healthy livestock but may harm young or weak livestock.

Livestock with access to fresh water or trough water would rarely be tempted to drink blackwater.

For more information about black water events and water quality visit Water Quality Australia.

Protecting water supplies from future contamination

It’s important to protect existing water supply quality to reduce future contamination by:

  • restricting stock access to water supplies
  • ensuring effluent application areas avoid water supplies and
  • diverting contaminated runoff away from water supplies and onto pasture.

For areas not inundated by flood water, it’s important to prepare for stock water needs. Having a livestock water supply, such as a tank or storage dam, located on higher ground can protect the farm from future contamination.

Page last updated: 25 Jan 2024