Skip links and keyboard navigation

Treatment systems for agriculture

Treatment systems can remove nutrients, sediments and pesticides from surface water or groundwater in agricultural areas and can also treat aquaculture wastewater.

A treatment train approach is required to achieve the best water quality outcomes. The first steps are to understand the site and where it sits in the landscape and to minimise or prevent pollutants entering the water through best management practices. Then water from production areas can be intercepted and treated through one or more treatment systems. Pollutants are removed from the water in sequence, from coarse-medium sediments to fine and dissolved pollutants (such as nutrients and toxicants).

A 9-step process describes how to identify, select and design treatment systems to improve farm water quality.

Vegetated drain on a sugar cane farm. Photo by Queensland Government

Quick facts

Treatment systems
can be cost-effective for improving water quality in Great Barrier Reef catchments and complement on-farm management practices and ecosystem repair[1][2].
If you have
any additional information on treatment systems or suggestions for additional technologies contact us via the feedback link at the bottom of the page.

Treatment systems for agriculture

Select from the tabs below

Select the blue text in the diagram for more information on each stage of a treatment train. The vital first stage in any treatment train is to develop a whole-of-system understanding

How Do I Plan and Design a Treatment Train?

Follow this 9-step process to plan and design a treatment train for water quality improvement:

  1. Understand your location: Develop a comrehensve understanding of the site and its sub-catchment/s to define clear objectives and ensure that a treatment train and/or treatment system is the most suitable management intervention. This is done via a desktop assessment and site visit and can be combined with a Walking the Landscape process.

    Tips and tricks: A site visit with the land holder or land manager is a great way to understand how the water flows, identify natural areas, discuss issues (drainage, erosion), identify production areas and possible sources and loss pathways for pollutants. This can be sketched on a map (Figure 1).

    The Whole-of-System, Values-Based Framework (the Framework) outlines the steps involved in developing the landscape understanding, defining objectives and identifying management options. If this framework identifies water quality improvement as an objective and an engineered solution such as a treatment system as a possible option, then proceed through the following steps. If the objectives are aquatic rehabilitation, refer to the Aquatic Ecosystem Rehabilitation Process.


    Figure 1: Identify all the sub-catchment boundaries and water regime at the site including overland flow, drainage lines and interaction with groundwater.


  2. Identify possible locations for treatment systems: Using the framework understanding, identify spaces where treatment systems could be located (Figure 2). This needs to consider the farming operations and areas the landholder would be willing to use for treatment systems. Areas of the farm not used for production or with low productivity could be considered in the first instance. Determine how cleaner water, potentially from undeveloped areas, could be separated out from water requiring treatment, to not overload the treatment systems.


    Figure 2: Identify the location and types of spaces available to locate treatment systems to incept water from the production area.


    Consider whether regional-scale treatment systems, treating water from multiple properties, would be a more cost-effective and feasible option within the catchment (Figure 3). It could be more cost effective to locate a large treatment system regionally, than on an individual farm, to share the costs of construction, operation and foregone production area among multiple entities. These regional treatment systems often replicate natural wetlands and their associated physical, biological and chemical treatment processes (refer to treatment wetlands, specifically landscape wetlands). These systems have the potential to provide multiple services such as habitat, flood mitigation, amenity and recreation, while ensuring the water treatment service is maintained.


    Figure 3: Investigate options for regional-scale treatment systems


  3. Identify suitable treatment systems: Review the pollutant removal processes for coarse-medium sediments, fine sediments, nutrients or other toxicants to identify which on-farm treatment systems may be suitable to trap the priority pollutants at the site. Each treatment system is made up of components that facilitate specific physical, biological or chemical processes. Understanding the way different treatment systems operate and their interaction with the landscape will help to identify suitable treatment systems. Consider the site and design requirements and cost of each relevant treatment system to determine its suitability for the site in terms of space, hydrology, access and available budget.
  4. Conduct a detailed assessment of the locations identified in step 2, with a technical specialist, including investigation of:
    • the water regime (hydrology) of the site or land unit and its connectivity to the sub-catchment/s and the broader catchment (if the site is within a floodplain)
    • topography
    • soils and geology
    • environmental values of surrounding area, including wetlands
    • production area and farming operations that may occur within or adjacent to the location
    • available space
    • access for construction and maintenance.
    • legislation or approvals that may be applicable at the site.
  5. Tips and tricks: A suitably qualified persion should be engaged to ensure that the treatment train delivers the desired water quality outcomes.

  6. Review and detailed design: Review each of the treatment systems identified (step 3); in the context of the detailed site assessment (step 4); to confirm:
    1. that the treatment train or treatment system contains the treatment processes required to meet the water quality objectives; and
    2. the location of the treatment system is suitable to meet objectives and avoids impacting other values and does not have off-site impacts
    3. which treatment system/s can proceed to the detailed design phase based on their suitability in meeting objectives and budget
    4. the landholder agrees with the concept and their responsibilities if the works proceed.

    If the water quality or landholder objectives are not fully met, then revisit steps 2 to 4 to select alternative management practices or treatment systems to meet objectives.

    Develop detailed design plans. Check it is likely to meet legislative requirements and submit any approval documents required.

  7. Determine costs and logistics: Develop budget, source construction contractors, obtain quotes and develop maintenance and monitoring plans.

    Ensure all construction, establishment, operation and maintenance costs are considered over the life of the treatment system and look at whether there is any financial or other support available, such as opportunities for equipment, materials or labour to be provided in-kind. Define and seek agreement with the person or organisation who will continue maintenance and monitoring of the structure over the life of the system. Liaise with relevant organisations (such as the local NRM or Landcare group) to identify support available.

  8. Final agreement and approvals: Obtain all approvals and final agreement of the landholder/s outlining expectations for construction, establishment and maintenance, preferably in writing.
  9. Implementation: Undertake construction and establishment. Manage construction process via strict hold points and supervision.
  10. Monitoring, maintenance and sharing: Implement the monitoring and maintenance plans developed in step 6. Consider any monitoring requirements to demonstrate the effectiveness and efficiency of the treatment train or treatment systems. Share the results and lessons from the project with the landholder and stakeholders.

Tips and tricks: Specific information on construction, establishment, monitoring and maintenance is available on each .


The content presented is based on published knowledge of treatment systems. Many of the treatment systems described have not been trialled in different regions or land uses in Queensland. The information will be updated as new trials are conducted and monitored. If you have any additional information on treatment systems or suggestions for additional technologies contact us via the feedback link at the bottom of the page.

Additional information

The Nature Conservancy – Leading at the edge: a roadmap to advance edge of field practices in agriculture

Beyond the Block fact sheet series, which focuses on water quality initiatives that can be applied on the 'edge of block' areas on farmland.

Farm drains and constructed wetlands as denitrifying systems - video

Minnesota Pollution Control Agency—Processes for removing pollutants from stormwater runoff

Minnesota Pollution Control Agency—Using the treatment train approach to BMP selection.

Townsville City Council—Water Sensitive Urban Design: design requirements for WSUD technologies in the coastal dry tropics

Wetland Technical Design Guideline

Wetland Management Handbook: Farm Management Systems (FMS) guidelines for managing wetlands in intensive agriculture

Bakers Creek Treatment Train - drone footage

Pages under this section


  1. ^ Eberhard, R, Thorburn, P, Rolfe, J, Taylor, B, Ronan, M, Weber, T, Flint, N, Kroon, F, Brodie, J, Waterhouse, J, Silburn, M, Bartley, R, Davis, A, Wilkinson, S, Lewis, S, Star, M, Poggio, M, Windle, J, Marshall, N, Hill, R, Maclean, K, Lyons, P, Robinson, C, Adame, F, Selles, A, Griffiths, M, Gunn, J & McCosker, K (2017), Scientific Consensus Statement 2017: A synthesis of the science of land-based water quality impacts on the Great Barrier Reef, Chapter 4: Management options and their effectiveness.. [online], State of Queensland, Queensland. Available at:
  2. ^ Kavehei, E, Hasan, S, Wegscheidl, C, Griffiths, M, Smart, JCR, Bueno, C, Owen, L, Akrami, K, Shepherd, M, Lowe, S & Adame, MF (22 November 2021), 'Cost-Effectiveness of Treatment Wetlands for Nitrogen Removal in Tropical and Subtropical Australia', Water. [online], vol. 13, no. 22, p. 3309. Available at: [Accessed 21 December 2021].

Last updated: 30 June 2022

This page should be cited as:

Department of Environment and Science, Queensland (2022) Treatment systems for agriculture, WetlandInfo website, accessed 13 April 2023. Available at:

Queensland Government
WetlandInfo   —   Department of Environment and Science