Indicators and how to select them for water/sediment quality management

​​​​​As part of the Water Quality Management Framework, you will:

Each line of evidence across the pressures, stressors and ecosystem receptors in the PSER causal pathway is represented by broad indicator types, and amongst these types are indicators from which you can select specific parameters for measurement.

More than one indicator may be selected and measured within each indicator type for each line of evidence. For example, biodiversity is an ecosystem receptor line of evidence for aquatic ecosystems that could be measured using multiple taxonomic groups, including macroinvertebrates, fishes and macrophytes.

Here we describe indicators for aquatic ecosystems and provide links to indicator information for other community values.

Indicators for aquatic ecosystems

Indicator selection depends on many factors, including:

  • types of pressures and associated stressors identified in the conceptual model
  • management goals
  • assigned levels of protection
  • spatial scale (broadscale, site-specific)
  • water type or medium (freshwater, marine water)
  • compartment (water or sediment)
  • ecosystem type (e.g. river or wetland)
  • location (e.g. wet–dry tropics, temperate coastal rivers of south-eastern Australia).

Factors to check when selecting indicators and lines of evidence within pressures, stressors and ecosystem receptors for aquatic ecosystems.

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Pressure lines of evidence are the drivers of change to the stressors affecting a water or sediment system. Pressures on aquatic ecosystems can come from many sources, such as:

  • agriculture and its associated stressors (e.g. pesticide effects or eutrophication from fertiliser use)
  • biota
  • climate change
  • land management and its numerous pressures and stressors (e.g. land clearing, stocking rates; irrigated area, acid sulfate soils, salinisation)
  • maritime activities and industries (e.g. anchoring, dredging, fishing, shipping)
  • mining
  • renewable energy developments
  • urban and industrial activities
  • water use.

Indicators for pressures should be quantifiable to enable comparisons with un-pressured and less-pressured systems. This will help you to make linkages between putative effects and likely causes through a weight-of-evidence evaluation. Those linkages, and the likely nature and extent of change in the indicator as a result of the expected level or intensity of the pressure, should be established via the current understanding (Step 1 of the Water Quality Management Framework).

This is how the sensitivity of the indicator can be adjudged as appropriate to the potential level of impact, and the statistical power of the monitoring program can be designed to sufficiently assess achievement of management goals.

Suitable measurements might be of loads or areal disturbance units, or even activity count data for a location. Examples of pressure indicators include:

  • annual loads of discharged salts or brines
  • areas of urban or mining development
  • hectares of clearing
  • human population measures
  • pesticide application rates (tonnes per km2)
  • pesticide sales
  • ship movement counts.


Chemical and physical line of evidence

Physical and chemical (PC) stressor and toxicant indicator types comprise concentration or strength measures that have both direct and indirect effects on ecosystems.

Direct PC stressors and toxicants have non-toxic and toxic direct effects on biota and ecosystems, and examples include:

  • non-toxic: nutrients (total N, inorganic N, organic N, total P, filterable reactive P, ammonia), chlorophyll a, temperature and turbidity
  • toxic: heavy metals, organics, ammonia, salinity, pH and dissolved oxygen (DO).

Indirect PC stressors and toxicants can modify the effects or toxicity of PC stressors or toxicants, examples and the effect of the indirect PC stressors and toxicants include:

  • pH changes can release metals
  • presence of dissolved organic carbon and suspended particulate matter can complex metals and reduce toxicity
  • temperature changes can alter physiological rates
  • DO changes can alter redox conditions

For some toxic stressors (e.g. metals), more detailed measurements might be required that target total vs dissolved forms, together with speciation and the bioavailable toxicant fraction.

See also:

Measurement of indicators from the chemical and physical line of evidence follow standard analytical procedures that specify the requirements for in situ vs laboratory measurements, sample collection, preparation and storage protocols, and analytical methods, including appropriate quality assurance/ quality control (QA/QC). All measurements must have detection limits that permit reliable comparisons of data with default guideline values (DGVs) for water quality.

A similar set of indicators apply to sediment samples. Additional co-stressor indicators include grain size and total organic carbon. Smaller grain size sediments have more binding sites, while organic carbon (OC) provides binding sites for organic contaminants. Normalisation to OC or grain size can account for differences in bioavailability when comparing to guideline values.

Non–water quality line of evidence

Indicator types within the non–water quality line of evidence that are not directly related to water quality might include invasive species, riparian condition, sedimentation and environmental flows. Some of these are only marginally removed from being considered as pressures. Some form of quantification will be required in the measurement programs for these indicators to ensure changes to biodiversity are not confounded by changes associated with these non–water quality stressors.

See also:

Ecosystem receptors

A set of ecosystem receptor indicators is available for each line of evidence within ecosystem receptors.

Biodiversity line of evidence

Management goals are typically linked to detecting changes at the population, community or ecosystem level of organisation. Indicators used for this purpose are classified together as ‘biodiversity indicators’. Such indicators are used to detect an ecosystem-level response to an effect, or to assess changes to biodiversity or conservation status. Biodiversity indicators may directly represent, or be surrogates for, these requirements.

Typical biodiversity indicators are:

  • species of high conservation value or species important to the integrity of ecosystems
  • communities of organisms, such as phytoplankton, macrophytes (also constituting important habitat), zooplankton, macroinvertebrates and fish, or
  • important ecosystem processes (e.g. measures of gross primary production and respiration).

Changes to biodiversity (populations and communities of organisms) may be manifested in both the short and longer term, depending on the biotic assemblage examined and the intensity of the stressor.

Some taxa and assemblages may be diagnostic for particular chemical and physical indicator types. For species and communities, typically changes to population or community structure are assessed at sites by way of comparison to a reference condition (baseline data and data from contemporaneously sampled control or reference sites).

Traditionally, taxa have been identified and enumerated by eye or using optical microscopy. Increasingly and into the future, effects on populations and communities will be more readily and efficiently assessed using improved ecogenomic techniques. Ecogenomics examines a broader range of taxa comprising micro-, meio and macro-organisms to identify operational taxonomic units (OTUs) that can be compared between sites.

Toxicity line of evidence

Toxicity determination reflects the direct effects of contaminant concentrations on one or more sensitive test organisms and is an important part of the toxicity line of evidence. Tests may be:

  • acute toxicity testing (a lethal or adverse sublethal effect that occurs after exposure to a chemical for a short period relative to the organism’s life span), or
  • chronic toxicity testing (lethal or sublethal effects over a substantial portion of the organism’s life span or an adverse effect on a sensitive early life stage).

Chronic effects are preferred for ecosystem protection in most circumstances.

Measurements of toxicity are compared to those on a matched water or sediment control from a toxicant-free reference site. The organisms’ response is the summation of the effects of all toxicants in the system, not only the target toxicant. The use of toxicity identification evaluation (TIE) procedures permit identification of particular classes of contaminants in the toxicant mix (Burkhard & Ankley 1989, USEPA 1992, 1993, Burgess et al. 2013).

Indicator responses will be the results of a number of acute or chronic bioassays using the test waters or sediments. For most assessments, chronic endpoints are preferred.

From the dose–response curves, the effective concentration (EC) or inhibitory concentration of 10% (IC10) values, or if possible no effect concentrations (NOECs), are determined. Although NOECs are no longer recommended (Warne et al. 2018).

Tests should compare test samples with a reference sample across a suitable dilution series. Appropriate QA/QC should involve the use of a reference toxicant, and measured toxicant concentrations during the tests.

Most toxicity testing is laboratory based in practice but field testing using caged organisms can be undertaken. The use of mesocosms, a semi-field approach, can assess toxicity to assemblages of species under controlled conditions.

For all selected toxicity testing indicators, you should choose the test endpoint — the specified measure of organism response — to be relevant and sensitive to the stressor(s) of concern identified in the conceptual model.

Biomarker line of evidence

Bioaccumulation indicator type

Bioaccumulation indicator types are measured concentrations of contaminants accumulated by aquatic biota from waters or sediments. These concentrations are compared with those in specimens from the same species from reference sites. The measurements indicate whether the contaminants are in forms that are bioavailable, and so complement measurements of chemical concentrations in waters and sediments.

Bioaccumulation can be measured in:

  • organisms collected from field sites where they are naturally present (passive biomonitoring)
  • caged organisms following field transplantation (active biomonitoring) (Maher et al. 2016)
  • caged organisms in the laboratory using microcosms.

Biomimetic devices can be used to estimate total body residues after exposure to complex mixtures of chemicals in waters or sediments (e.g. Simpson et al. 2012, Ghosh et al. 2014, Huynh et al. 2015) and may be preferable where the organisms of interest are highly mobile, or variable in their propensity to accumulate or excrete the contaminants of concern.

You may measure contaminant concentrations in whole organisms, or in specific organs or tissues of the sampled species. If organisms are small, then you may pool samples of whole organisms (or tissues) to reduce variability and analytical costs, but modern instrumentation can achieve acceptable limits of resolution for small tissue samples (< 1 g) in many instances.

We provide advice on procedures for sample collection, preparation and storage and of appropriate QA/QC. Results are reported as either wet weight or dry weight concentrations and it is important to also report moisture content.

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Biomarkers of exposure and effect indicator type

A biomarker is a measurable indicator of a suborganism biological effect, condition or response. Biomarkers can be indicators of exposure to, or effects due to, contaminants in waters and sediments. They can be measured in the laboratory, or in organisms that have been exposed to contaminants in the field or laboratory.

The biological endpoints comprise molecular, biochemical, physiological or histopathological markers, as summarised by Hook et al. (2014) and Kroon et al. (2017). When viewed in conjunction with other indicator types within different lines of evidence, biomarkers of exposure and effect can provide useful confirmation of potential effects (Hook et al. 2014).

Biomarkers provide an early warning of impending environmental problems that may later manifest as toxicity. Results can be obtained rapidly, typically within 24 to 48 hours of collection of organisms. As such, biomarker responses are typically seen at concentrations below those for toxicity.

Although they may be indicative of some type of physiological impairment as a consequence of exposure to one or more contaminants or to some other non-chemical stressors, it is often difficult to demonstrate the significance of this effect on the health of the organism and extrapolation to longer‐term effects on ecosystem health.

Indicators for other community values

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Cultural and spiritual values

We provide detailed information about the importance of cultural and spiritual values, including indicators, in other guidance.

Primary industries

We cover indicators for water resources used in primary industries in other guidance.

Human drinking water

Indicators for drinking water are measurements of chemical and biological contaminant concentrations, and associated PC stressor parameters.

The health authorities of Australia and New Zealand are primarily responsible for management of drinking water quality in those countries. Refer to the guidance for Australia and New Zealand in:

Recreational water

Indicators for recreational waters include chemical and biological contaminants with thresholds defined by human health impacts.

The National Health and Medical Research Council (NHMRC) published Guidelines for Managing Risks in Recreational Water to protect human health from threats posed by the recreational use of coastal, estuarine and freshwaters, such as natural and artificial hazards. It includes key aspects of the World Health Organization (WHO) Guidelines for Safe Recreational Water Environments and combines much of the international consensus on healthy recreational water use with current understanding of Australian waters, to provide guidance relevant to local conditions. The NHMRC recreational water guidelines supersede previous guidance, such as the ANZECC & ARMCANZ (2000) guidelines and the NHMRC’s Australian Guidelines for Recreational Use of Water.

Guidance for New Zealand’s recreational waters are available in Ministry for the Environment’s Microbiological Water Quality Guidelines for Marine and Freshwater Recreational Areas.

Advice for selecting indicators in aquatic ecosystems

These key factors that will help you determine the lines of evidence and indicators to measure in a particular situation, based on the information you gathered in Steps 1, 2 and 3 of the Water Quality Management Framework.

Choose diagnostic indicators from different lines of evidence

The lines of evidence identified from the quality of evidence tables completed in Step 3 are a culmination of decisions based on the prioritised water or sediment quality issues likely to affect ecosystems. These issues are drawn from the likely pressures and stressors affecting, or having the potential to affect, ecosystems, and the ecosystem receptors in the system that are likely to respond.

From the lines of evidence you have identified, select the precise indicators and measurements to be made by considering:

  • the most sensitive mode of action of the stressor and the most sensitive ecosystem receptors of that action (highlighted in the conceptual model completed in Step 1 of the framework)
  • diagnostic value of the indicator
  • practicalities of monitoring the indicator in the local environment, including capacity of the measurement program to detect a change to the effect size for ecosystem receptor indicators with prescribed statistical power.

For example, if agricultural development (pressures) has potential to result in nutrient enrichment of receiving waters, then measurement of nutrients (stressors) and plants (any form of algae, macrophytes) (ecosystem receptors) may be the obvious priority indicator types for selection and measurement.

While there are no real constraints on the indicators and parameters to be used within each line of evidence, you should chose diagnostic indicators under the circumstances of the issue of concern to be as effective as possible.

See also:

Account for spatial and temporal scales

Selection of stressors and ecosystem receptors needs to be targeted to the spatial and temporal scale of the potential response to the activity or pressure.

The Water Quality Guidelines recognise different indicator types for finer-spatial scale and broadscale assessments.

Indicator selection for broadscale assessments has been reviewed by Dafforn et al. (2016) and deserves special mention. Such assessments are typically conducted over wide geographical areas for first-pass determination of the extent of a problem or potential problem (broadscale land-use issues, diffuse-source effluent discharges or information for State of Environment Reporting), screening of sites, or to assess results from large-scale remediation efforts (ANZECC & ARMCANZ 2000).

For broadscale assessments, ecosystem receptor biodiversity line of evidence may typically apply rapid assessment techniques (e.g. AUSRIVAS). For stressors, you will need water quality, hydrological, climate and other environmental data gathered from recorders or samples collected from a network of monitoring stations at a suitable sampling frequency. Increasingly, data for pressure and stressor indicators at these large spatial scales, including remote locations, are being acquired from remote (including satellite) and proximal sensing (e.g. sea surface temperature and chlorophyll a, mapping of vegetation type and habitat loss).

Indicators and associated measurements should also be collected over carefully selected timescales so that the data will provide a time-integrated history of the system (Dafforn et al. 2016). Humphrey et al. (1995), for example, described a tiered approach to biological monitoring in Magela Creek, Northern Territory:

  • Early detection of possible (mine-related) effects arising over the short term (within the wet season of concern) using in situ toxicity testing (freshwater snail reproduction).
  • Early detection of possible effects arising as a summation of wet-season exposures using bioaccumulation of metals in freshwater mussels.
  • Detection of both post–wet season and longer-term effects over years using natural fish and macroinvertebrate communities.

Choose indicators to suit the water, ecosystem and medium

Different indicators are available for:

  • water type — inland waters (including freshwater) versus coastal marine waters
  • different ecosystem types
  • medium compartment (water or sediment).
  • Water type, ecosystem types and medium compartment for default guidance, guideline values and indicators provided in the Water Quality Guidelines are shown in Figure 2. Where site-specific guideline values are derived, water, ecosystem and compartment types will be broadest and will generally align with those described against physical and chemical stressors in Figure 2.

Relevant indicator types are described in the Water Quality Guidelines for:

Figure 2 Classification of ecosystem type for each of the broad categories of indicator types (in grey text boxes)

Seek regional-specific advice on indicators

The ecoregional schema developed for aquatic ecosystems in Australia and New Zealand will eventually provide important regional-specific advice on indicators through Your location. Where information is available, you will find proven indicators that have been successfully and routinely monitored for specific pressures for different ecosystem types in the region.

Use indicators as surrogates or measures of management goals

Indicators within the biodiversity line of evidence may be selected as surrogates or direct measures of the management goals, ecosystem attributes that are locally important to protect. Such indicators can inform management of the extent to which ecosystems are being protected or are tracking towards improved ecosystem condition.

Include ecosystem receptors to target higher levels of protection

Section of the ANZECC & ARMCANZ (2000) guidelines provided recommendations on the number and mix of indicators that could be used in integrated monitoring for each of the ecosystem conditions.

For sites of high conservation value, the ANZECC & ARMCANZ (2000) guidelines recommended:

  • direct toxicity assessment (DTA) to determine a safe dilution wherever effluents are to be discharged
  • water and sediment PC stressors
  • an ‘early detection’ biological receptor indicator for either water or sediment (whichever is deemed to harbour greater risks to aquatic organisms arising from the fate and persistence of waste substances)
  • a quantitative biodiversity indicator
  • a community metabolism indicator, if applicable and available.

Prediction and early detection of possible effects in sites of high conservation value are important so that substantial and ecologically important effects can be avoided. Such information may be provided via in situ toxicity testing or use of biomarker indicators.

For slightly to moderately disturbed systems, and wherever possible, indicator selections similar to those applied for sites of high conservation value were recommended.

For highly disturbed systems, water and sediment toxicants and PC stressors, together with biodiversity assessment at coarse taxonomic discrimination, may suffice for many water/sediment quality assessments.


ANZECC & ARMCANZ 2000, Australian and New Zealand Guidelines for Fresh and Marine Water Quality, Australian and New Zealand Environment and Conservation Council and Agriculture and Resource Management Council of Australia and New Zealand, Canberra.

Burgess RM, Ho KT, Brack W & Lamoree M 2013, Effects-directed analysis (EDA) and toxicity identification evaluation (TIE): Complementary but different approaches for diagnosing causes of environmental toxicity, Environmental Toxicology and Chemistry 32: 1935–1945.

Burkhard LP & Ankley GT 1989, Identifying toxicants: NETAC's toxicity-based approach, Environmental Science and Technology 23: 1438–1443.

Dafforn KA, Johnston EL, Ferguson A, Humphrey C, Monk W, Nichols SJ, Simpson SL, Tulbure MG & Baird DJ 2016, Big data opportunities and challenges for assessing multiple stressors across scales in aquatic ecosystems, Marine and Freshwater Research 67: 393–413.

Ghosh U, Kane Driscoll S, Burgess RM, Jonker MT, Reible D, Gobas F, Choi Y, Apitz SE, Maruya KA, Gala WR, et al. 2014, Passive sampling methods for contaminated sediments: practical guidance for selection, calibration, and implementation, Integrated Environmental Assessment and Management 10: 210–223.

Hook SE, Gallagher EP & Batley GE 2014, The role of biomarkers in the assessment of aquatic ecosystem health, Integrated Environmental Assessment and Management 10: 327–341.

Humphrey CL, Faith DP & Dostine PL 1995, Baseline requirements for assessment of mining impact using biological monitoring, Australian Journal of Ecology 20(1): 150–166.

Huynh T, Harris HH, Zhang H & Noller BN 2015, Measurement of labile arsenic speciation in water and soil using diffusive gradients in thin films (DGT) and X-ray absorption near edge spectroscopy (XANES), Environmental Chemistry 12(2): 102–111.

Kroon F, Streten C & Harries S 2017, A protocol for identifying suitable biomarkers to assess fish health: A systematic review, PLoS ONE 12(4): e0174762.

Maher WA, Taylor AM, Batley GE & Simpson SL 2016, Bioaccumulation, in: Sediment Quality Assessment; A practical guide, 2nd Edition, Simpson SL & Batley GE (eds), CSIRO Publishing, Clayton, pp 123–156.

Simpson SL, Yverneau H, Cremazy A, Jarolimek CV, Price HL & Jolley DF 2012, DGT-induced copper flux predicts bioaccumulation and toxicity to bivalves in sediments with varying properties, Environmental Science & Technology 46: 9038–9046.

USEPA 1992, Toxicity Identification Evaluation: Characterization of Chronically Toxic Effluents, Phase I, United States Environmental Protection Agency, Washington DC.

USEPA 1993, Methods for Aquatic Toxicity Identification Evaluations: Phase III Toxicity Confirmation Procedures for Samples Exhibiting Acute and Chronic Toxicity, United States Environmental Protection Agency, Washington DC.

Warne, MStJ, Batley GE, van Dam RA, Chapman JC, Fox DR, Hickey CW & Stauber JL 2018, Revised Method for Deriving Australian and New Zealand Water Quality Guideline Values for Toxicants, Australian Government Department of Agriculture and Water Resources, Canberra.