Protocols for biological assessment

The National Environmental Monitoring Standards are being developed to ensure consistency for monitoring applications throughout New Zealand. Development of this website is ongoing.

Protocols for field sampling of freshwater fish in both wadeable (Joy et al. 2013) and non-wadeable (Hicks 2013) habitats have been published.

The National Policy Statement for Freshwater Management (New Zealand Government 2017) mandates the use of the Macroinvertebrate Community Index (MCI) (Stark & Maxted 2007) for freshwater macroinvertebrates. Policy Objective CB1(aa) requires councils develop a monitoring plan that includes macroinvertebrate community monitoring. Under Policy Objective CB3, every regional council must:

• use the MCI
• establish methods under Policy CB2 to respond to an MCI score below 80, or a declining trend
• ensure the methods:
  • investigate the causes of declining trends or where the MCI score is below 80
  • seek to halt declining trends
  • seek to improve an MCI score if it is below 80, unless this is caused by naturally occurring processes, pest or unwanted organism, or by infrastructure listed in Appendix 3 of New Zealand Government (2017).

Additional guidance relevant to New Zealand includes:

• protocols for sampling macroinvertebrates in wadeable streams (Stark et al. 2001)
• stream periphyton monitoring manual (Biggs & Kilroy 2000)
• Sediment Assessment Methods, which provides protocols and guidelines for deposited fine sediments in flowing waters (Clapcott et al. 2011)
• community-based (i.e. ‘Citizen Science’) protocols are given in the Stream Health Monitoring and Assessment Kit (NIWA 2016).

New Zealand users should be aware that frameworks and tools continue to be updated and developed (e.g. Macroinvertebrate metrics for the National Policy Statement for Freshwater Management (Clapcott et al. 2017)). Consequently, users should consult with relevant agencies to ensure that the biological protocols adopted are consistent with best practice and current policy.

National level biological assessment protocols exist for both freshwater and marine ecosystems and, as noted through the subsequent sections, can be recommended or adopted by the states and territories. A summary list is provided below.

• The Australian River Assessment System (AusRivAS) is a prediction system used to assess the biological health of Australian rivers, developed under the National River Health Program (NRHP) in 1994. AUSRIVAS has two streams, Bioassessment and Physical assessment, with the former providing protocols for macroinvertebrate assessment. The AusRivAS website provides access to protocols, training as well as regional (state and territory) AusRivAS models.
   
• The National Environmental Science Program (NESP) Marine Biodiversity Hub has published field manuals for marine sampling (Przeslawski & Foster 2020). The primary aim of the manuals is to ensure that data collected by marine sampling platforms at different times and places across Australia are directly comparable. They include, but are not limited to, protocols for sampling via autonomous underwater vehicles, different methods of videography and different towed approaches.
   
• Survey guidelines for threatened fish species (SEWPaC 2011) have been published to provide guidance for the assessment of Australia’s threatened fish species under the Environment Protection and Biodiversity Conservation Act 1999.
   
• The National Investigation and Reporting Protocol for Fish Kills (Commonwealth of Australia 2007) encourages a consistent national approach in the response to major fish kill incidents in freshwater, estuarine and marine waters. The protocol aims to streamline the investigation and reporting of major fish kill incident, and sets out the recommended minimum requirements for each stage of the management of a fish kill incident, including preparedness, investigation and reporting activities.

At the time of writing, no specific protocols had been identified for the Australian Capital Territory (ACT). Typically, the national or New South Wales (NSW) protocols are adopted in the ACT.

The NSW Department of Planning, Industry and Environment – Water Group uses a range of indicators and monitoring programs to track and assess river health (DPIE 2020).  These indices focus on freshwater inland and coastal rivers above the tidal limit. 

The NSW Department of Planning, Industry and Environment – Environment, Energy and Science Group focuses on the use of ANZG (2018) and AusRivAS for assessing estuarine waterway health (Department of Planning, Industry and Environment 2019), and brief advice is provided for macroinvertebrate sampling. An example of water quality monitoring reporting is provided for one regional area (Midcoast Council 2018), within which some details are provided about specific methods.

Other NSW Government agencies such as Department of Primary Industries – Fisheries and the Environmental Protection Agency may also carry out monitoring programs and should be consulted as needed for appropriate protocols.

General advice for using the ANZECC/ARMCANZ (2000) Guidelines for NSW is provided here. Note that this document was published in 2006 and has not been updated to reflect the current Australian and New Zealand Guidelines for Fresh and Marine Water Quality (ANZG 2018). Consequently, it should be read in conjunction with ANZG (2018).

The use of AusRivAs modelling is discouraged in the Northern Territory; however, the collection and sample processing methods prescribed in Lloyd and Cook (2001) and Lamche (2007) are applicable to stream assessment where appropriate when coupled with rigorous experimental design.

AUSRIVAS procedures for family-level Northern Territory models are described in the Northern Territory AusRivAs sampling and processing manual (Lloyd and Cook 2001), and for genus-level (and family-level) in the Darwin-Daly regional AusRivAs models (Lamche 2007). Methods for the assessment of condition of riparian zones are described in Dixon et al. (2006).

The Supervising Scientist Branch of the Commonwealth Department of Agriculture, Water and the Environment undertakes annual biological monitoring in receiving waters downstream of the Ranger uranium mine. Protocols for toxicity monitoring (early detection) and quantitative macroinvertebrate sampling (biodiversity assessment) are provided in Supervising Scientist Division (2011, 2013).

Several biological indicators that are relevant to water and sediment quality have protocols described in the Queensland Government Water monitoring and sampling manual (DES 2018). Queensland’s WetlandInfo site (DES 2020) contains a full assessment toolbox with a filterable search function enabling identification of multiple assessment techniques. Additionally WetlandInfo contains a list of approved inventory methods in Queensland.

Additionally, the following protocol from ANZECC/ARMCANZ (2000) is currently applicable in Queensland:

• 8.1.2.1 Stream, Lakes and Wetlands – Algae, Macroinvertebrates, Freshwater Fish, Turtles and Community Metabolism (although often modified for specific regional report cards), including Methods 3A(ii), (iii), (iv), (v) and 3B.

The Great Barrier Reef Marine Park Authority (GBRMPA) has a number of different biological monitoring protocols including the Reef 2050 Water Quality Improvement Plan Marine Monitoring Program (GBRMPA 2020), Eye on the Reef (GBRMPA 2011) and Incident Response (GBRMPA 2013) monitoring protocols. Endorsed protocols are available at the GBRMPA ELibrary.

As with other Australian State and Territory regulations, a number of the Queensland protocols assume that the user has the necessary permits (e.g. general fisheries permit), ethics and scientific use approvals to use them. This may include, for example, an exemption to default bag limits, such as for molluscs or particular fish species, depending on the needs of the monitoring program.

The South Australian Environment Protection Authority drives the aquatic ecosystem monitoring and reporting program in marine water and inland surface waters (EPA South Australia 2020).

The use of AusRivAS (Method 3A(i) in ANZECC/ARMCANZ (2000)) is discouraged, although rapid assessment of macroinvertebrates via a rapid field pick under Method 3A(ii) is still applicable.

The Environment Protection Authority (EPA South Australia 2018) has provided details on the rationale and method for the assessment of South Australian inland waters (rivers and creeks) and this is used in its statewide monitoring, evaluation and reporting program.

The Tasmanian Environmental Protection Authority provides overviews of water quality issues and monitoring programs (EPA Tasmania 2013) and guidance for biological monitoring (Environment Protection Authority 2020), while the Department of Primary Industries, Parks, Water and Environment provides information on assessing river health (DPIPWE 2016a).

The health of waterways is assessed using standard bioassessment methods based on the Tasmanian River Condition Index (NRMSouth 2009) and AusRivAS. The Tasmanian River Condition Index includes rapid biological assessment protocols for algae, macroinvertebrates (based on AusRivAS), fish and riparian vegetation. The intended uses of the index are itemised in DPIPWE (2016b), and links to various protocols are provided.

Contextual information (e.g. degree of flow modification) that could be helpful in selecting indicators can be found in the Conservation of Freshwater Ecosystem Values Database.

Users in Victoria should consult with the relevant agencies (e.g. Environment Protection Authority Victoria) to ensure that protocols adopted for biological indicators are consistent with current policy and guidance.

Victorian EPA has developed the following relevant publications:

• The rapid biological assessment methodology for rivers and streams (EPA Victoria 2003) is to be used whenever rapid bioassessment is to be undertaken for purposes required by the Environment Protection Act 1970. (This publication replaces publication 604, which was issued in June 1998.)
   
• The environmental quality guidelines for Victorian lakes (EPA Victoria 2010) identifies indicators and their values for assessing the ambient condition of Victorian lakes. Managers are encouraged to use the methods outlined in this manual and provide feedback to the Environmental Protection Authority Victoria to further develop them.
   
• Similarly, the environmental water quality guidelines for Victorian riverine estuaries (EPA Victoria 2011) provides a framework and tools for assessing their environmental condition. It provides guideline values that describe the condition of reference-quality estuaries, which can be used as an indicator for the assessment of other estuaries. This publication describes the development and use of these indicators.
   
• Risk based sediment quality assessment guidelines have been adopted (SEPP Waters 2018) for freshwater, estuarine and marine sediments, based on an adaptation of the methods in Simpson and Batley (2016).
   
• Additionally the Victorian Algal Management Framework (DELWP 2018) provides guidance on the preparedness and response arrangements for harmful algal bloom coordination within Victoria.

Rapid biological assessment protocols for freshwater macroinvertebrates under AusRivAS are provided in the Western Australia AusRivAS sampling and processing manual (van Looij 2009).

Rapid biological assessment protocols for fish and crayfish within south-west waters are provided as part of the South-west Index of River Condition (SWIRC) by the Department of Water (Storer et al 2020b). The SWIRC also incorporates standard methods for collection of information (field and desktop) needed to support species expectations or to diagnose changes in aquatic communities (summary provided in Storer et al 2020a). Sampling protocols for particular fish species are available through the Environment Protection and Biodiversity Conservation Act 1999 threatened fish sampling protocols (SEWPaC 2011).

Apart from particular programs, such as monitoring the health of Cockburn Sound (Environmental Protection Authority 2005), there are no compulsory protocols for marine water. Some general guidance for indicator selection is provided in a technical guidance document for protecting the quality of Western Australia’s marine environment (Environmental Protection Authority 2016).

The WA Department of Primary Industries and Regional Development maintains a Fish Kill Response Manual for the investigation and management of fauna mortality events in fresh, estuarine and marine waters. The manual contains protocols and procedures for sampling water and affected biota and is used by relevant State Government agencies. While it is not published, it can be requested from DPIRD at the following email address: fishkill@dpird.wa.gov.au.

Additionally, the following protocols from ANZECC/ARMCANZ (2000) are currently applicable to marine waters in Western Australia:

• 8.1.1.1 Broadscale assessment of ecosystem ‘health’, seagrass shoot density and depth limit
• 8.1.1.2 Early detection of acute and chronic changes including benthic infauna community composition (marine), coral health (marine) and Method 9
• 8.1.2.2 Marine and estuarine systems Methods 6 and 7.

Guidance and advice for selecting and monitoring suitable biological indicators to assess pressures from dredging and related activities will be forthcoming. The guidance will be based on research completed in 2019 through the Dredging Science Node of the Western Australian Marine Science Institution (WAMSI 2014). This research identified and quantified the critical pressure fields associated with dredging programs and the responses of key biota to those pressures.

The Murray–Darling Basin Authority generally does not develop protocols, preferring to rely on national guidance. However, for cyanobacteria counts, comparison values are included in the Basin Plan in Section 9.18 (Commonwealth of Australia 2018), which provides reference to the National Health and Medical Research Council Guidelines for Managing Risks in Recreational Water (NHMRC 2008). For all other physical and chemical water quality targets, the Murray–Darling Basin Authority refers to national guidelines.

However, the Sustainable Rivers Audit program (MDBC 2004) used some biological indicators for water quality characterisation between 2004 and 2006. Table 2 of MDBC (2004) identified the indicators used, with subsequent sections and tables of the report providing additional detail. This was not a protocol; rather, it was a framework that allowed use of the best available information to characterise water quality, consistent with the principles of the ANZG (2018) Water Quality Management Framework.

Anderson, JT & Davis, CA (eds) 2013. Wetland Techniques, Volume 2, Organisms. Springer Netherlands, Dordrecht. Accessed 12 April 2017.

ANZECC/ARMCANZ 2000. Australian and New Zealand guidelines for fresh and marine water quality. National Water Quality Management Strategy Paper No 4. Australian and New Zealand Environment and Conservation Council, Agriculture and Resource Management Council of Australia and New Zealand, Canberra, ACT, Australia.

ANZG 2018. Australian and New Zealand Guidelines for Fresh and Marine Water Quality. Australian and New Zealand Governments and Australian state and territory governments, Canberra, ACT, Australia.

ANZG 2020. Ecosystem receptor indicators. Australian and New Zealand Guidelines for Fresh and Marine Water Quality. CC BY 4.0. Australian and New Zealand Governments and Australian state and territory governments, Canberra, ACT, Australia.

Biggs, BJF & Kilroy, C 2000. Stream periphyton monitoring manual. Prepared for the New Zealand Ministry for the Environment. National Institute for Water and Atmospheric Research, Christchurch, New Zealand.

CCME 2011. Protocols manual for water quality sampling in Canada. Canadian Council of Ministers of the Environment. Accessed 6 March 2018.

Clapcott J, Wagenhoff, A, Neale, M, Storey, R, Smith, B, Death, R, Harding, J, Matthaei, C, Quinn, J, Collier, K, Atalah, J, Goodwin, E, Rabel, H, Mackman, J & Young, R 2017. Macroinvertebrate metrics for the National Policy Statement for Freshwater Management. Prepared for the Ministry for the Environment. Cawthron Report No. 3073, Cawthron Institute, Nelson, New Zealand.

Clapcott, JE, Young RG, Harding JS, Matthaei CD, Quinn JM & Death RG 2011. Sediment Assessment Methods: Protocols and guidelines for assessing the effects of deposited fine sediment on in-stream values. Cawthron Institute, Nelson, New Zealand.

Commonwealth of Australia 2007. National Investigation and Reporting Protocol for Fish Kills. Australian Government Department of Agriculture, Fisheries and Forestry, Canberra, ACT.

Commonwealth of Australia 2018. Basin Plan 2012. Commonwealth of Australia, Canberra, ACT.

Davies, J, Baxter, J, Bradley, M, Connor, D, Khan, J, Murray, E, Sanderson, W, Turnbull, C & Vincent, M 2001. Marine Monitoring Handbook. Joint Nature Conservation Committee, Peterborough, United Kingdom. Accessed 6 March 2018.

DELWP 2018. Algal management framework, Victorian Blue-Green Algae Circular. Department of Environment, Land, Water and Planning, Melbourne, Victoria, December 2018.

Department of Environment and Primary Industries 2013. Port Phillp Bay marine algal bloom response plan. Government of Victoria, Melbourne, Victoria.

Department of Planning, Industry and Environment 2019. Monitoring and reporting on water quality. NSW Government. Accessed 23 June 2020.

DES 2018. Monitoring and Sampling Manual: Environmental Protection (Water) Policy. Department of Environment and Science Government, Brisbane, Queensland.

DES 2020. WetlandInfo. Department of Environment and Science Government, Brisbane, Queensland. Accessed 12 August 2020.

Dixon, I, Douglas, M, Dowe, J & Burrows, D 2006. Tropical Rapid Appraisal of Riparian Condition, Version 1 (for use in tropical savannas). River and Riparian Land Management Technical Guideline Number 7, Land and Water Australia, Canberra.

DPIE (2020). Water in New South Wales – River Health. Department of Planning, Industry and Environment, Sydney, NSW. Accessed 12 August 2020.

DPIPWE 2016a. Assessing river health. Department of Primary Industries, Parks, Water and Environment, Government of Tasmania. Accessed 24 June 2020.

DPIPWE 2016b. Tasmanian River Condition Index. Department of Primary Industries, Parks, Water and Environment, Government of Tasmania. Accessed 24 June 2020.

Environmental Protection Authority 2005. Manual of standard operating procedures: For environmental monitoring against the Cockburn Sound environmental quality criteria (2003–2004). A supporting document to the State Environmental (Cockburn Sound) Policy 2005. Environmental Protection Authority Report 21. Environmental Protection Authority, Perth, Western Australia.

Environmental Protection Authority 2016. Technical Guidance – Protecting the Quality of Western Australia’s Marine Environment. Environmental Protection Authority, Perth, Western Australia.

Environment Protection Authority 2020. Technical Guidance for Water Quality Objectives (WQOs) Setting for Tasmania. Environment Protection Authority, Hobart, Tasmania.

EPA South Australia 2018. Rationale and method for the assessment of inland waters (rivers and creeks) in South Australia. Government of South Australia, Adelaide.

EPA South Australia 2020. Monitoring. Government of South Australia, Adelaide. Accessed 24 June 2020.

EPA Tasmania 2013. Water. Government of Tasmania, Hobart. Accessed 24 June 2020.

EPA Victoria 2003. Rapid bioassessment methodology for rivers and streams. Guideline for Environmental Management. Publication 604.1. EPA Victoria, Melbourne, Victoria.

EPA Victoria 2010. Environmental quality guidelines for Victorian lakes. Publication 1302. EPA Victoria, Melbourne, Victoria.

EPA Victoria 2011. Environmental quality guidelines for riverine estuaries. Publication 1347.1. EPA Victoria, Melbourne, Victoria.

GBRMPA 2011. Eye on the Reef weekly monitoring training manual. A complete guide to monitoring your site. Great Barrier Reef Marine Park Authority, Townsville, Queensland.

GBRMPA 2013. Reef Health Incident Response System Second Edition. Great Barrier Reef Marine Park Authority, Townsville, Queensland.

GBRMPA 2020. Marine monitoring program. Great Barrier Reef Marine Park Authority, Townsville, Queensland.

Gibson, GR, Bowman, ML, Gerritsen, J & Snyder, BD 2000. Estuarine and Coastal Marine Waters: Bioassessment and biocriteria technical guidance. EPA 822-B-00-024, US Environmental Protection Agency, Office of Water, Washington, DC.

Hauer, FR & Lamberti, GA (eds) 1996. Methods in stream ecology. Academic Press, San Diego.

Hicks, A 2013. Fish surveys in non-wadeable systems. Environment Southland, Invercargill, New Zealand.

Joy, M, David, B & Lake, M 2013. New Zealand freshwater fish sampling protocols. Part 1 Wadeable rivers and streams. The Ecology Group – Institute of Natural Resources, Massey University, Palmerston North, New Zealand.

Lamche, G 2007. The Darwin-Daly regional AUSRIVAS models – Northern Territory. User Manual. Report 06/2007D. Aquatic Health Unit, Department of Natural Resources, Environment and the Arts, Darwin.

Lloyd, J & Cook, S 2001. Northern Territory AUSRIVAS. Australian River Assessment Scheme: sampling and processing manual. Northern Territory Department of Lands, Planning and Environment, Darwin.

MDBC 2004. Sustainable Rivers Audit Program. Murray–Darling Basin Commission, Canberra, Australia.

Midcoast Council 2018. Midcoast Council waterway and catchment report. Midcoast Council Natural Systems, Forster, NSW.

New Zealand Government 2017. National Policy Statement for Freshwater Management 2014. Updated August 2017 to incorporate amendments from the National Policy Statement for Freshwater Amendment Order 2017. New Zealand Government, Wellington.

NHMRC 2008. Guidelines for Managing Risks in Recreational Water. National Health and Medical Research Council, Canberra, ACT.

Nichols, SJ , Barmuta, LA, Chessman, B, Davies, PE, Dyer, FJ, Harrison, ET, Hawkins, CP, Jones, I, Kefford, BJ, Linke, S, Marchant, R, Metzeling, L, Moon, K, Ogden, R, Peat, M, Reynlodson, TB & Thompson, RM. 2017. The imperative need for nationally coordinated bioassessment of rivers and streams. Marine and Freshwater Research, 68(4), 599–613.

NIWA 2016. Stream health monitoring and assessment kit. National Institute for Water and Atmospheric Research, Auckland, New Zealand. Accessed 23 June 2020.

NRMSouth 2009. The Tasmanian River Condition Index Aquatic Life Field Manual. NRMSouth, South Hobart, Tasmania.

Przeslawski R & Foster S [Eds.] 2020. Field Manuals for Marine Sampling to Monitor Australian Waters, Version 2.Report to the National Environmental Science Program, Marine Biodiversity Hub. Geoscience Australia and CSIRO, Canberra, Australia.

SEWPaC 2011. Survey guidelines for Australia’s threatened fish: Guidelines for detecting fish listed as threatened under the Environment Protection and Biodiversity Conservation Act 1999. Commonwealth of Australia, Canberra.

Simpson, SL & Batley, GE 2016. Sediment Quality Assessment. CSIRO Publishing. Accessed 28 October 2016.

Stark, JD & Maxted, JR 2007. A User Guide for the Macroinvertebrate Community Index. Prepared for the Ministry for the Environment. Cawthron Report No.1166. Cawthron Institute, Nelson, New Zealand.

Stark, JD, Boothroyd, IKG, Harding, JS, Maxted, JR & Scarsbrook, MR 2001. Protocols for sampling macroinvertebrates in wadeable streams. New Zealand Macroinvertebrate Working Group Report No.1. Prepared for the Ministry for the Environment. Sustainable Management Fund Project No. 5103. Ministry for the Environment, Wellington, New Zealand.

Storer, T, White, G, O’Neill, K, Galvin, L & van Looij, E 2020a. The South West Index of River Condition, Method overview 2020, River Science Technical Series 1, Healthy Rivers program, Department of Water and Environmental Regulation, Perth. In press.

Storer, T, White, G, O’Neill, K, Christie, E, Galvin, L % van Looij, E 2020b. The South West Index of River Condition, Method summary – Aquatic biota 2020, River Science Technical Series 2, Healthy Rivers program, Department of Water and Environmental Regulation, Perth. In press.

Supervising Scientist Division 2011. Environmental monitoring protocols to assess potential impacts from Ranger minesite on aquatic ecosystems: In situ toxicity monitoring – freshwater snail, Amerianna cumingi, reproduction test. Internal Report 588, March. Supervising Scientist, Darwin.

Supervising Scientist Division 2013. Environmental monitoring protocols to assess potential impacts from Ranger minesite on aquatic ecosystems: Macroinvertebrate community structure in streams. Internal Report 591, July 2013. Supervising Scientist, Darwin.
Valentine, JP, Jensen, M, Ross, DJ, Riley, S & Ibbott, S 2016. Understanding broad scale impacts of salmonid farming on rocky reef communities. Fisheries Research and Development Corporation, Hobart, Australia.

van Looij, E 2009. WA AUSRIVAS sampling and processing manual. Water Science Technical Series Report No. 13. Department of Water, Perth, Western Australia.

WAMSI 2014. Dredging Science Node. Western Australian Marine Science Institution, Perth, Western Australia. Accessed 24 June 2020.