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Treatment systems for agriculture

Different treatment systems are available for improving water quality in agricultural production landscapes. Each type of treatment system works to remove specific pollutants from either surface or groundwater with different levels of efficiency.

A treatment train approach is required to achieve the best water quality outcomes. A treatment train works by first preventing or minimising pollutants entering the water system through best management practices. Then ‘cleaner’ water, from undeveloped areas, is diverted away so that 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 soluble pollutants (such as nutrients and toxicants). The characteristics of the landscape and the type of pollutant to be treated are key considerations when selecting a treatment system for improving water quality.

Sugar cane. Photo by Queensland Government

Quick facts

systems can be important for improving water quality in Great Barrier Reef catchments as a complement to on-farm management practices and ecosystem repair[1].
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.


Select the train carriages for more information on each stage of a treatment train. The vital first stage in any treatment train is to understand your location.


How Do I Plan and Design a Treatment Train?


  1. Understand your location: Develop a complete understanding of the site and its sub-catchment/s to ensure that the treatment train and treatment system/s are designed to cost-effectively treat priority pollutants, keeping with landholder objectives and relevant regulations. The "Wetland site management and rehabilitation" pages include a set of information sources that can assist with this process.

    Define the site and the sub-catchments (Figure 1) and determine:

    1. 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)
    2. location and connectivity of farm land and drainage (surface and groundwater) relative to natural wetlands and waterways and artificial drainage systems
    3. characteristics of the site and sub-catchment/s (size, land use, geology/soils, topography, vegetation) and identify any potential site constraints (potential for Acid Sulfate Soils, bedrock, steep site etc.)
    4. pollutants being generated in the agricultural landscape (type, quantity and concentration)
    5. water quality objectives (refer to planning documents such as Water Quality Improvement Plans - contact the local NRM group)
    6. the landholder’s objectives, farming operations and any constraints
    7. any planning constraints, regulations or planning instruments that may restrict or support the use of treatment systems (including funding or grants available).

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


  3. Farm and Waterway Best Management Practices (BMP): Ensure BMPs are adopted throughout the farm to:
    1. reduce the amount of pollutants generated on the farm, such as nutrients and pesticides excess to crop requirements
    2. slow down and minimise the amount of water leaving the farm (minimising pollutant transport)
    3. protect downstream treatment systems from pollutant overloading.

  5. Identify possible locations for a treatment train or treatment systems: Identify the location and type of spaces available where treatment systems may be located (Figure 2). This needs to take into account the farming operations and identify which areas the landholder would be willing to use for treatment systems. Determine how cleaner water, potentially from undeveloped areas could be separated out from water requiring treatment, so as to not overload the treatment systems.

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


  7. 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 in the agricultural landscape. Ensure design criteria and site constraints are considered. Each treatment system is made up of components that facilitate specific physical, biological or chemical processes, so understanding the way different treatment systems operate and their interaction with the landscape will help in identifying suitable treatment systems or a treatment train. Consider cost of different treatment systems and investigate whether regional scale treatment systems, treating water from multiple properties, would be a more cost-effective and a feasible option within the catchment (Figure 3).

    Figure 3: Investigate regional scale treatment systems


  9. Conduct a detailed assessment of the locations identified in step 3, including:
    1. water regime, including irrigation practices
    2. topography
    3. soils and geology
    4. environmental values of surrounding area, including wetlands
    5. production area and farming operations that may occur within or adjacent to the location
    6. available space
    7. access for construction and maintenance.

  11. Review and detailed design: Review each of the treatment systems identified (step 4); in the context of the detailed site assessment (step 5); to confirm that the treatment train or treatment system contains all the treatment processes required to meet the water quality objectives. Conduct detailed designs and ensure it will meet legislative requirements and that there will be minimal adverse environmental impacts from the proposal. If the water quality objectives are not fully met, then revisit steps 2 to 4 to select alternative management practices of treatment systems to meet objectives.

  13. Determine costs and logistics: 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. Liaise with relevant organisations (such as the local NRM group) to identify support available.

  15. Final agreement and approvals: Obtain all approvals and final agreement of the surrounding landholder/s outlining expectations for construction, establishment and maintenance (including cost considerations), preferably in writing.

  17. Monitoring: Consider any monitoring requirements to demonstrate the effectiveness and efficiency of the treatment train or treatment systems.


It is often necessary and desirable to engage a treatment system specialist, to ensure that the treatment train delivers the desired water quality outcomes.


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

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

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

A systematic approach for the comparative assessment of stormwater pollutant removal potentials

Water Environment Research Foundation—Critical assessment of stormwater treatment and control selection treatment

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

Building a Bioreactor Bed in the Wet Tropics

Wet Tropics Waterways Podcast on Constructed Wetlands

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:

Last updated: 3 October 2018

This page should be cited as:

Department of Environment and Science, Queensland (2018) Treatment systems for agriculture, WetlandInfo website, accessed 13 May 2021. Available at:

Queensland Government
WetlandInfo   —   Department of Environment and Science