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Developing a reef water quality management plan — case study

​​​​​​​​​​​​​This case study has been contributed by the Great Barrier Reef Marine Park Authority and reflects the opinions of that organisation

A water quality management plan is a whole-of-catchment approach that uses the ​Water Quality Management Framework to develop adaptive management strategies to protect the community values of catchment waterways.​

About the site

The Great Barrier Reef Marine Park stretches along 2300 km2 of Queensland coast, in the Coral Sea. It comprises more than 3000 individual reefs, 600 continental islands, 300 coral cays and 150 inshore mangrove islands over an area of 344,400 km2.

The Great Barrier Reef contains many important marine habitats, ranging from shallow inshore areas (with seagrass, mangroves, algal and sponge gardens and inter-reefal communities) to deep oceanic areas more than 250 km offshore. Its natural beauty attracts people from around the world.

In 1981 UNESCO listed the reef as a World Heritage Site to help protect its high ecological value ecosystems.

Pressures affecting the health of sensitive ecosystems along the coast and reefs include:

  • ​climate change
  • direct use for fishing and tourism
  • farming and grazing practices in the catchment area
  • modifications to the catchment and coastline from past decision-making
  • urban development for intensive uses.

Our challenge

The main issue is that healthy coral reefs can be vulnerable to algal encroachment when they are weakened through the actions of acute disturbances, such as:

  • bleaching events (release of intracellular endosymbionts by stressed coral)
  • cyclones
  • outbreaks of crown-of-thorns starfish.

Historically, an algal reef had the power to recover its health. But we are now experiencing more cyclone clusters, large-scale bleaching events and more frequent crown-of-thorns starfish outbreaks in the Great Barrier Reef so that it’s becoming more difficult for a reef to recover.

We are working towards enhancing the resilience of the Great Barrier Reef to recover from these acute disturbances or adapt to chronic stressors, such as climate change.

The key premise of the Reef Water Quality Protection Plan (Reef Plan) is that improving the quality of catchment runoff to the reef waters is the best way to improve the reef’s resilience.​

Applying the Water Quality Management Framework

The Australian Government (including the Great Barrier Reef Marine Park Authority), the Queensland Government and key stakeholders developed the first Reef Plan in 2003 and will release the fourth Reef Plan in 2017. These 4 plans will represent multiple cycles through the Water Quality Management Framework. We call this cyclical process adaptive management or ‘learning by doing’.

This case study focuses on the development and release of the second Reef Plan in 2009 through to the release of the first annual Report Card in 2011, a process similar to those used for all 4 reef plans.

The 2011 Report Card measured our progress in achieving water quality objectives in the Great Barrier Reef lagoon from the 2009 baseline, across indicators for management practices, catchment condition, catchment pollutant loads and marine condition, such as seagrass and reef health (key coastal ecosystems that the Reef Plan aims to protect).

This case study makes reference to more recent developments in science and monitoring that are being used to improve the fourth Reef Plan.

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Examine current understanding

What do we know about the threats to the Great Barrier Reef and how to manage them?

We developed conceptual models to assist in showing the key reef components and processes, how the threats impact on them and how we are managing those threats.

To do this, we used existing data and scientific information contributed by research institutions, government agencies, universities, commercial companies and consultants, stakeholders, traditional owners and community members.

We documented our current understanding of the issues facing the reef in the Scientific Consensus Statement 2008 (PDF 1.9 KB). This built on the first scientific consensus published by Baker et al. (2003), and synthesised more than 500 papers reporting on the science behind the reef, including outcomes from environmental research programs. We articulated how we had been managing those issues in the 5-year Reef Water Quality Protection Plan 2003 (PDF 1.8 MB).

In the Great Barrier Reef Outlook Report 2009 (PDF 20 MB), we reported on the status of the reef and its management, and identified the 4 greatest risks to the reef as:

  • catchment runoff
  • climate change
  • development of coastal land
  • direct use, including fishing and tourism.

We knew that 95% of the water quality problems in the reef lagoon came from agricultural runoff, particularly:

  • nutrients and pesticides from cane-growing properties and other farms
  • sediments and attached nutrients from grazing properties.

The scope of Reef Plan 2009 was therefore to address non-point (diffuse) source pollution (different sources that cannot be attributed to one point of dispersal) from broad-scale land use. This included agriculture (cropping, grazing, horticulture and forestry) and other tenures of public land (national parks and reserves).

The first 3 reef plans did not focus on management actions for urban land uses due to its small and localised contribution to relevant pollutant loads and existing regulation of point source discharges. As progress has been made with the diffuse source pollution, the fourth Reef Plan is being expanded to more specifically include urban loads not addressed by regulations (e.g. runoff from new developments).

The water quality in the reef lagoon is mainly impacted by runoff events, which happen more regularly in the tropical wet season than the tropical dry season, and the diffuse source pollutants they carry.

A runoff event during the wet season (Figure 1a) results in loads of nutrients, pesticides and sediments (mainly due to bank, gully and hillslope erosion in cropping and grazing systems) being delivered to the reef lagoon.

Most of the sediments drop out near the coast but finer sediments can travel longer distances and influence light conditions in some areas further offshore. Where light availability improves after the sediment drops out, the more available nutrients encourage the growth of algae in the reef lagoon. Then the water quality gradually improves further away from the coast, towards the mid and outer shelf areas. So the water quality issues associated with catchment runoff are mainly coastal (inshore marine environment).

During the dry season (Figure 1b) when catchments receive little or no rainfall, we observe reworking of the finer sediments in the system by the actions of wind waves and tides.

Figure 1. Conceptual model of agricultural runoff issues for the Great Barrier Reef during (a) wet season and (b) dry season. Source: Great Barrier Reef Marine Park Authority

Looking at the impacts of wet season runoff events in more detail (Figure 2), we can see why poor water quality can slow the recovery of coral reefs and seagrasses from increased catchment loads and other disturbances:

  • turbid waters reduce light for photosynthesis in corals and seagrasses
  • sediment can smother seagrass, and smother and kill some corals
  • herbicides can inhibit photosynthesis
  • fungicides and insecticides can impact coral early life cycle stages
  • nutrient-related phytoplankton blooms may promote juvenile crown-of-thorn starfish, resulting in adult population outbreaks that can rapidly reduce coral cover
  • nutrients and particulate organic matter may result in a dominance of macroalgae over coral
  • lack of productive marine herbivores can result in algae-dominated reefs
  • turbid waters reduce the depth that coral can grow, and reduce coral photosynthesis and recruitment
  • bleaching events and cyclones can rapidly reduce coral cover.

Figure 2. Impact of catchment runoff on the Great Barrier Reef during the wet season. Source: Great Barrier Reef Marine Park Authority


Key concepts:

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Define community values and management goals

What types of specific management goals did we set to protect the aquatic ecosystems (our key community value) in the Great Barrier Reef lagoon?

The Great Barrier Reef is World Heritage listed and has an ecosystem condition of high conservation value, which requires the highest level of protection. It’s very important that we work to protect the coral reefs and areas of seagrasses, which provide habitats for lots of marine species. Figure 3 shows the extensive network of reefs that comprise the Great Barrier Reef and the spatial extent of the shallow and deep water seagrass beds.

Figure 3. Coral reefs and areas of seagrass in the Great Barrier Reef, 2013. Source: Great Barrier Reef Marine Park Authority

Community values

The highly valued aquatic ecosystems in the coral reefs and the lagoon and sea-floor environments represent a key community value for the region. The Great Barrier Reef waters also have high recreational, commercial fishing and cultural and spiritual values, which are not the focus of Reef Plan.

Management goals

Reflecting on the ecological significance of the region, the key management goal is to protect and improve the ecosystems of the Great Barrier Reef waters, with specific goals to protect and improve the identified areas of coral reefs and seagrasses.

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Define relevant indicators

Which indicators did we select to protect the aquatic ecosystems in the reef lagoon from loads of nutrients, pesticides and sediments coming from the catchment areas?

From our conceptual models, we obtained multiple lines of evidence for the causes of high loads of nutrients, pesticides and sediments coming from important land uses in the catchment through to their impact on reef water quality and health (Table 1).

Table 1. Relevant indicators selected for Great Barrier Reef to assess and monitor inshore marine condition

Lines of evidenceIndicators
Pressure (land use management practices) Adoption of better land use and management practices
  • Grains management practice score
  • Grazing management practice score
  • Horticulture management practice score
  • Sugarcane management practice score
  • Bare Ground Index
Stressors (loads of nutrients, pesticides and sediments from catchment runoff) Nutrients
  • Total nitrogen load at end-of-catchment and end-of-subcatchment areas
  • Pesticide load at end-of-catchment and end-of-subcatchment areas
  • Sediment load at end-of-catchment and end-of-subcatchment areas
Ecosystem receptors (health of coral reefs and seagrass areas, reef lagoon water quality) Coral reef health
  • Coral cover
  • Macroalgae cover
  • Coral juveniles
  • Coral cover change
Seagrass health
  • Seagrass abundance
  • Reproduction effort
  • Nutrient status
Water quality
  • Chlorophyll a
  • Total suspended solids

We measured each of these indicators in the Paddock to Reef Integrated Monitoring, Modelling and Reporting Program, to evaluate and report on the effectiveness of Reef Plan.

To implement, integrate and report on these indicators, we undertook (Figure 4):

  • paddock-scale water quality and economic monitoring and modelling via
  • surveying adoption of improved land management practices
  • plot-scale rainfall simulations
  • water quality monitoring of key pollutants under improved management practices
  • catchment-scale water quality monitoring and modelling via
  • water flow and water quality monitoring of key pollutants at subcatchment and end-of-catchment sites (to calibrate the catchment models)
  • wetland mapping
  • remote sensing of groundcover and riparian areas
  • marine-scale water quality monitoring and modelling via
  • remote sensing of water quality in pollutant flood plumes
  • grab sampling of water quality during flood events
  • water quality loggers and passive samplers
  • seagrass abundance and health monitoring
  • coral reef health monitoring.

Figure 4. The Integrated Paddock to Reef Integrated Monitoring, Modelling and Reporting Program uses cutting-edge monitoring and modelling tools that links across each of the scales (paddock, catchment and marine) to enable reporting in the short-to-medium term. *Marine WQ model was developed in 2016 and will be used as part of reporting in the fourth Reef Plan.


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Determine water quality guideline values

How did we determine water quality guideline values for each of the water quality indicators we selected for the reef lagoon?
We were fortunate that the Great Barrier Reef Marine Park Authority (GBRMPA) had already developed the Water Quality Guidelines for the Great Barrier Reef Marine Park. These guidelines describe the concentrations or guideline values (trigger values) for sediments, nutrients and pesticides necessary for the protection and maintenance of marine species and ecosystem health in the Great Barrier Reef.

To develop the guideline values, the GBRMPA-commissioned study used existing site-specific information for chlorophyll a and turbidity (including consideration of biological effects data and reference site water quality data; refer to De’ath & Fabricius 2008), as well as methods for developing pesticide guideline values in the ANZECC & ARMCANZ (2000) guidelines.

Over time since 2008, the science behind the GBRMPA’s water quality guideline values has greatly improved and they are currently being reviewed and updated.

Key concepts:

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Define draft water quality objectives

Guideline values were selected for relevant indicators to protect the aquatic ecosystem community value.

Other community values were not the focus of the management plan but in most cases they will be protected by the guideline values selected for aquatic ecosystems because these values will be the most stringent.

At this point, the guideline values became draft water quality objectives with an aim to be met by 2020.

Noting that the longer term ‘goal’ of Reef Plan 2009 was to ensure that by 2020 the quality of water entering the reef from adjacent catchments has no detrimental impact on the health and resilience of the Great Barrier Reef.

In Step 8, these water quality guideline values helped us to derive what the pollutant load levels and management practices should be to meet our water quality objective.

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Assess if draft water objectives are met

What did the monitoring data show about where our draft water quality objectives were met or not?

Depending on the outcome of this assessment, we had different options:

  • if they were met — continue management and monitoring to ensure protection of the marine environment
  • if they were not met — ramp up management actions to improve water quality.

We were fortunate to have good monitoring data for some of the key indicators across multiple lines of evidence in the reef lagoon, such as levels of chlorophyll a (an indicator for algal growth; Figure 5) and secchi disc depth (an indicator for water clarity; refer to De’ath & Fabricius 2008).

Some areas in the northern region of the Great Barrier Reef were in close to pristine conditions and the chlorophyll a monitoring data showed that we were maintaining them below the guideline value of 0.45 µg/L associated with this ecosystem of high ecological value.

In some areas of the reef lagoon, the guideline value for chlorophyll a had been exceeded and we did not meet the draft water quality objective. This meant that we needed to improve current conditions to achieve the water quality objective, or to at least start the improvement process back towards the water quality objective by setting, for example, a 5-year management goal for Reef Plan 2009 (refer to Steps 8 and 9).

Figure 5. Estimated spatial distribution of chlorophyll a in the Great Barrier Reef (a) northern region and (b) southern region, 2009. Source: Great Barrier Reef Marine Park Authority


Key concepts:

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Consider additional indicators or refine water quality objectives

A catchment-scale water quality management plan like this is typically based on current understanding and monitoring and updated every 5 to 7 years. We would not invest in refining the water quality objectives or coming up with additional indicators at this step.

This step is more relevant to management decisions about specific major new discharges (e.g. industrial or mining developments) in areas where relevant understanding and monitoring is not available.

Instead, we looked at improving any information we needed during the life of the plan. We would revise or add indicators, as required, or improve the water quality guideline values as part of the next planning cycle.

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Consider alternative management strategies

What could have been done differently to increase the chance of achieving the water quality objectives?

Before we could answer this, we needed to review our existing management strategies and continue with those that were working (e.g. preventing problems from future development).

We used our existing communication mechanisms to engage with our stakeholders (Figure 6) about possible future management strategies or scenarios for the next 5 years and assess their cultural, economic, social and water quality implications. Out of that stakeholder involvement process, we assessed a range of scenarios, and negotiated and prioritised agreed management actions for the next Reef Plan.

Figure 6. Institutional arrangements for Reef Plan 2009


As indicated in Step 5, the water quality objectives/guideline values (i.e. the Reef Plan ‘goal’) helped us to derive what the water quality ‘load’ levels and management practices should be to meet our water quality objectives.

Reef Plan 2009 targets for water quality:

  • a minimum 50% reduction in annual average total nitrogen loads at the end of catchments by 2013
  • a minimum 20% reduction in annual average total sediment loads at the end of catchments by 2020
  • a minimum 50% reduction in annual average pesticide loads at the end of catchments by 2013.

Reef Plan 2009 targets for land and catchment management:

  • 80% of sugarcane growers will have adopted improved management practices by 2013
  • 80% of horticulture producers will have adopted improved management by 2013
  • 50% of landholders in the grazing sector will have adopted improved management practices by 2013
  • a minimum 50% late dry season groundcover on grazing lands.

Modelling used to compare scenarios

To help assess the water quality implications of our management practice scenarios we undertook paddock and catchment modelling to determine load reductions from improved management practices. For example, if all land managers moved from current poorer practices (D, C and B classes) to best practices (A class). This allowed us to estimate the water quality (load) improvement for each scenario.

Then we determined potential water quality (concentration) improvements in the reef lagoon for each scenario and compared those concentrations with the water quality guideline values. For Reef Plan 2009, we used empirical relationships to convert water quality catchment loads (e.g. dissolved inorganic nitrogen) into water quality concentrations (e.g. chlorophyll a) to compare against the water quality guideline values and calculate the required load reductions.

Typically in this assessment and negotiation process, a range of scenarios are run to cover strategies from current management practices to all ‘A class’ practices, as well as changing existing land uses to less polluting land uses. This allows stakeholders to see and discuss the range of water quality (load) improvements across the scenarios at the same time as discussing the cultural, economic and social implications — supported by any such complementary assessments — of each scenario.

Our negotiations resulted in an agreed set of management actions to improve water quality loads, and hence reef lagoon concentrations, to either meet the water quality objectives or move towards achieving them.

At the same time, our paddock monitoring trials and models allowed us to estimate the most effective management practices and help set management practice targets aimed at achieving the agreed water quality load targets.

In the fourth Reef Plan, we are replacing use of empirical models at this assessment stage with the eReefs Environmental Modelling Suite. Using the temporal and spatial information in eReefs will strengthen our predictions about the catchment loads required to meet the water quality guideline concentrations.

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Assess if water quality objectives are achievable

For a catchment-scale water quality management plan, this step is typically done in conjunction with Step 8.

The cultural, economic, social and water quality assessments of all alternative management scenarios were done together and presented to and discussed with stakeholders. This helped us to make a collective decision about what management strategies would be implemented over the life of the plan to achieve or work towards achieving the water quality objectives.

If the assessments showed that the water quality objectives could be achieved and the cultural and spiritual, economic and social impacts were acceptable to stakeholders, then we could continue to Step 10 and implement the management strategy. For Reef Plan 2009, this was achieved in some spatial areas.

For the inshore areas affected by river plumes, we expected a gradual improvement over time. This meant that we had to accept incremental improvements in water quality towards the desired ‘management goals’ (from Step 2) over time by implementing agreed actions in the next 5 years of the plan that were affordable, and culturally and socially acceptable.

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Implement agreed management strategy

Over time, we continue to improve the way we develop and implement Reef Plan.

In the first years of Reef Plan 2003, we developed and implemented 10 broad strategies with 65 management actions based on what people were doing at the time. For the second and third reef plans, and continuing on into the next 5 years, we’ve been operating within 3 strategic work areas to implement the plan.

  • Prioritising investment and knowledge — using the best science to prioritise where we implement management actions and which are the most cost-effective actions to implement, as well as ongoing research, and prioritising, collaborating, funding, evaluation and synthesising research and monitoring programs, including producing the 5-yearly scientific consensus statement to inform each Reef Plan review.
  • Responding to challenge — where the bulk of the work occurs, implementing actions to achieve improvements in water quality and eventually reef health, and working with key stakeholders (farmers and graziers) to help them improve management practices.
  • Evaluating performance — measuring our success using the Paddock to Reef Integrated Monitoring, Modelling and Reporting Program.

Our annual report card to stakeholders reports on progress towards our management practice and water quality load targets, as well as reef water quality and health.

As expected, we see improvements in management practices first, then improvements in loads, and then improvements in reef water quality and health.

For nutrient and sediment impacts, these improvements will take 10 years or more because of the historical loads still in the system.

However, reductions in pesticide loads should result in water quality improvements in the receiving waters over the short term.

Great Barrier Reef regional water quality improvement plans

Reef Plan is an example of a well-funded adaptive management strategy to protect one of Australia’s World Heritage sites.

In the same way that Reef Plan is a good example of a catchment-based water quality management plan, it is supported by 6 ‘regional’ water quality management (improvement) plans that are also good examples:

These 6 plans provide more regionally specific strategies, using Reef Plan as the overarching plan to provide context and address reef-wide issues. These regional plans were first developed between 2002 and 2009 and were updated between 2014 and 2016.

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