Identifying the water quality and ecosystem health threats to the Torres Strait from the Fly River runoff

Jane Waterhouse

Simon Apte

Led by: Jane Waterhouse, JCU / Simon Apte, CSIRO


Project Summary

Runoff from the Fly River in Papua New Guinea (PNG) influences water quality conditions in the Torres Strait region. Recent work (NESP Project 2.2.1 and 2.2.2) has clearly demonstrated that this influence is largely constrained to the northern Torres Strait, as far east as Bramble Cay and at least as far west as Boigu Island. The southern extent of influence is considered to be limited to within 40-50km of the PNG coast in the western areas, and around 80km in the eastern areas. The intensity of this influence, and the potential ecological impacts, are still not well understood. Trace metal concentrations are higher in the northern Torres Strait around Boigu and Saibai, however it is not clear whether this enrichment is natural or the result of mine derived inputs of trace metals. Further investigation is required to understand the prevalence and frequency of the extension of the Fly River plume into the northern Torres Strait, and further characterisation of plume constituents, particularly sediment and trace metals in comparison to previous results including the Torres Strait Baseline Study.


Project Publications
Final Report
Journal Article
Island Summary – Bramble Cay
Island Summary – Erub
Island Summary – Masig
Island Summary – Saibai, Boigu
Island Summary – Warraber, Iama, Poruma





Project Description

What is the problem?

Work conducted in the first phase of NESP Tropical Water Quality Hub Projects 2.2.1 and 2.2.2 has provided greater certainty of the extent and frequency of the influence of runoff from the Fly River in PNG on important marine ecosystems in the Torres Strait. It is now feasible to conclude that the influence of the Fly River and associated sediments, particulate materials and trace metals is focused in the north eastern Torres Strait and along the PNG coast to the west, particularly during the southeast trade wind season (~May to December). This conclusion is drawn from multiple lines of evidence including in-situ analysis of trace metals in the water column and sediment, the analysis of freshwater influences in coral cores at Bramble Cay and Erub Island (1781-1993), hydrodynamic modelling of the Fly River discharge, analysis of remote sensing imagery (2008-2017) for turbidity and exposure patterns, local weekly salinity monitoring several central and northern locations (variable timing, 2016 to present), deployment of continuous turbidity loggers at Bramble Cay and Masig Island (2016-2018), analysis of microbial community composition and a pilot study of metals in seagrass leaves. The results are also supported by previous studies in the region.

Our water quality data showed that water quality in the Torres Strait is generally excellent. However, slightly elevated concentrations of trace metals were observed in the northern Torres Strait around Boigu and Saibai Islands. For example, out of 12 water samples collected in this region 10 exceeded the ANZECC 99% species protection water quality guideline value for dissolved copper of 0.3 µg/L. No samples exceeded the 95% water quality guideline of 1.3 µg/L which is commonly used by regulators across Australia. The source of the metals enrichment is likely to comprise natural trace metal inputs from the Papua New Guinea land mass possibly augmented by dissolved and particulate trace metals originating from the Ok Tedi mine in Papua New Guinea (Fly River discharge). Further field work is required to confirm the magnitude and sources of the trace metals in the northern Torres Strait, and importantly develop predictions of future metal concentrations in this region over the duration of mine life.

Key objectives

Building on the studies conducted as part of NESP Projects 2.2.1 and 2.22, we propose to continue a multidisciplinary approach to quantify the levels of trace metals and sediments at different times of year and identify the sources of trace metals to the northern Torres Strait. The objectives are:

  1. To quantify the levels of trace metals and sediments in the northern Torres Strait, with a focus on the marine areas around Boigu and Saibai Islands, the Warrior Reefs, Masig Island and Bramble Cay in 2019.
  2. To identify the sources of trace metals in these areas and distinguish probable inputs from local sources or the Fly River.
  3. To assess the implications and potential risks of the findings to marine ecosystems and local communities.

How Research Addresses Problem – methodology

The investigations will combine the following techniques to meet the objectives.

Project inception planning worksho

The project team have not had the opportunity to fully engage with key stakeholders and receive their considered input into this project. We plan to embrace the concept of project co-design and will arrange a project planning workshop as the first step of this project.Support from the Torres Strait Regional Authority (TSRA) is critical to the success of this project. The workshop will first involve dissemination of the new knowledge generated from our NESP Round 2 projects followed by sessions designed to collect information on future needs from stakeholders. This information will be used to refine the project design.

Field surveys and tracing of trace metals in waters, sediments and some bioindicator organisms (Project 2.2.2): Purpose – To provide a more comprehensive understanding of the trace metal concentrations found in the northern Torres Strait (including Boigu, Saibai and the Warrior Reefs) across seasons, and assess the ecological relevance of these concentrations and potential implications for the local communities. Methods to identify the sources of trace metals in these areas and distinguish probable inputs from local sources or the Fly River will also be established.

Team: Simon Apte, Brad Angel, Chad Jarolimek, CSIRO

Major tasks:

  1. Characterising trace metal distributions in the Northern Torres Strait: Our previous NESP project identified significant trace metal gradients in the Torres Strait. Generally water quality is excellent across the region, however the highest concentrations of several trace metals including copper were found around the Boigu and Saibai Islands. We now intend to focus further on characterising trace metal concentrations in the northern Torres Strait. This will be achieved by conducting a major field campaign in which water and sediment samples will be taken along a transect running from close to the mouth of the Fly River Estuary) to the northwest bounds of the Torres Strait. Water and sediment samples will be analysed for a comprehensive range of parameters including copper, mercury and organic carbon concentrations. The sampling campaign will also include seagrass sampling in the Warrior Reef region. In order to provide temporal information, the major field campaign will be supplemented by two smaller focussed surveys around Boigu and Saibai. Logistical support from the TSRA will be sought for this activity. The CSIRO team have already worked successfully with TSRA Rangers based on Boigu and Saibai and conducted a water quality survey in June 2018.
  2. Development of methods for tracing mine-derived sediments in the Torres Strait: A tracing technique will be developed which enables the detection of mine-derived sediments originating from the Ok Tedi mine in suspended and benthic sediments in the Torres Strait. Through their contacts at the Ok Tedi copper mine, CSIRO will obtain mine tailings samples and water large volume water samples from Lewada which is at the freshwater end-member of the Fly River Estuary and using these samples to derive a method for detection of mine sediments in marine systems. These samples will be procured independently by CSIRO and will be free of cost to the project. Suspended sediments will be isolated and pre-concentrated from the water samples by filtration and centrifugation. A number of analytical approaches will be trialled. These include multi-elemental analysis (63 trace elements will be determined, scanning electron microscopy and high resolution X-Ray diffraction.

This work builds on previous studies conducted by the CSIRO group which have successfully developed tracer methods for mine-derived sediments originating from two mines in PNG (Porgera gold mine and the Wafi Golpu copper mine).

  1. Fly estuary plume tracking: The method developed in Task 2 will be applied to both benthic and suspended sediment samples collected in the field campaigns described above to determine the amount of sediment originating from the Ok Tedi mine. This information will allow us to gain an understanding of current mine-derived sediment transport across the Torres Strait. The method will also be applied to archived sediment cores collected during our first NESP project in the Torres Strait.

Collection of anecdotal evidence of plume intrusions (Project 2.2.2): Purpose – To gain further insight to the views of the local community regarding the influence of the Fly River into the Torres Strait. To date, interviews have been conducted by Cass Hunter from CSIRO with community members from Boigu and Saibai. This effort would be extended to include other areas of interest and engage scientists in the team with long term experience in the region such as Jon Brodie or Simon Apte, and preferably a staff member from TSRA. This additional input will provide an opportunity for knowledge exchange in the discussion process.

Team: Jane Waterhouse and Jon Brodie, JCU; Simon Apte, CSIRO; TSRA if possible

  1. Visit island communities at Saibai, Boigu, Masig and Erub to provide feedback of the existing results (to be conducted prior to the end of 2018) and commence further discussions with local community members at Masig and Erub to gain initial insights of anecdotal evidence of the influence of the Fly River in the region.
  2. Liaise with TSRA to develop an appropriate approach to gain further insights from the local communities through the extension period.

In-situ loggers for salinity and turbidity: Purpose – To provide real time meteorological, salinity and turbidity data, operate stations at Bramble Cay and Masig Island (both continuing with addition of salinity), Saibai Island and the northern Warrior Reefs (both new with addition of salinity) to assist in assessing the temporal variability in the frequency of exposure of brackish and turbid waters. This will provide continuation or commencement of real time meteorological and turbidity data for indicators of Fly River intrusions and in-situ parameters for model runs (see below). Turn-over of the real time ocean temperature loggers in the region will continue for understanding and measuring coral bleaching conditions.

The initial data and hydrodynamic model runs show that there are events where coastal PNG waters can influence the waters in the northern Torres Strait such as around Bramble Cay and occasionally down to the central Torres Strait such as at Masig Island. The data are not of enough length to reliably filter out local in-situ events (such as the re-suspension of local material through local wind conditions or low salinity events from localised rainfall) and so the collection of additional data will strengthen the understanding of what conditions promote the influx of PNG water into northern Torres Strait.

Team: Scott Bainbridge, AIMS

Major tasks:

  1. Install new Saibai and Warrior Reef Stations, redeploy instrumentation at Masig Island and Bramble Cay with the addition of salinity meters.
  2. Annual service for all Ocean Stations.
  3. Logger exchanges for all Ocean Stations.
  4. Data analysis and reporting including provision of data to the project team to assist in cross correlation of water quality results, and where possible, validation of the sediment model.

Local salinity monitoring: Purpose – To continue weekly salinity monitoring by TSRA Rangers at northern locations in the Torres Strait to link results to the logger data where applicable, and provide local data from additional locations. Presently, salinity monitoring is conducted at Boigu, Saibai, Erub, Masig, Iama, Poruma and Warraber Islands. It would be desirable to continue this effort in these locations, with priority for Boigu, Saibai, Erub and Masig. We will also explore the application of the simple ‘Eye on the Water’ phone application to measure Forel Colour Classification (linked to the remote sensing true colour analysis) which could be collected during routine Ranger activities where possible / appropriate. *While discussions have commenced, the proposed arrangements for this with TSRA are yet to be finalised. This component also provides an avenue for local engagement and capacity building of TSRA Rangers.

Team: Jane Waterhouse and Caroline Petus, JCU and TSRA Rangers

Major tasks:

  1. Provider refresher training to TSRA Rangers participating in the salinity monitoring, and the ‘Eye on the Water’ phone application to measure Forel Colour Classification (linked to the remote sensing true colour analysis) if applicable. Provide feedback to each team currently conducting salinity monitoring of results to date.
  2. Continue to maintain contact with the Rangers conducting the monitoring and ensure that all equipment is maintained and supplied.
  3. Analyse and interpret the results in the context of the model outputs and in-situ continuous loggers.

Remote sensing of river plumes: Purpose- To extend the 10 year dataset of satellite remote sensing data of plume movement, turbidity and frequency of the exposure of turbid waters in the northern Torres Strait. The additional field data will increase the confidence of the results. This data will assist in linking the in-situ data to potential sources, distinguishing between local and Fly River influences, and assessing changes between 2008 and 2020.

Team: Caroline Petus, Dieter Tracey and Jon Brodie, JCU

Major tasks:

  1. Update the satellite (MODIS) true colour database and process satellite colour class maps up to 2020.
  2. Use newly collected in-situ water quality measurements of TSS concentrations, turbidity and salinity to validate the satellite colour classification and increase the confidence in remote sensing results. Analyse cloud cover data to assess potential influence of cloud presence on seasonal patterns.
  3. Process other and/or higher resolution satellite images (e.g. Sentinel data) in addition to the MODIS images to give further insight into the very near-shore (Warrior Reef, Saibai, Boigu area), as well as the Fly, Wassi kussa and Mai kussa river plume mixing fronts.
  4. Further analyse the satellite databases to understand the prevalence and frequency of exposure of Bramble Cay to the Fly River waters (influence of wind intensity and direction).
  5. Provide satellite remote sensing data to give a spatial context to in-situ observations (loggers, salinity, seagrass monitoring) in near real time.
  6. Provide satellite remote sensing data for the Risk assessment to ecosystems and communities.
  7. Provide satellite remote sensing data to assist in training the sediment transport model (Year 2 task).

Sediment transport modelling: Purpose – To assess the transport of Fly River sediment (and its associated particulate metals) in the Torres Strait region. Field data are available from the in-situ loggers, in-situ data (recent work plus Wolanski’s 1990s studies) and potentially remote-sensing. The model will assist to predict changes in the distribution of particulate material from the Fly River over time.

Fly River pollutants consist of trace metals and fine sediment ; they enter Torres Strait during the trade wind season in two ways, (1) dissolved metals in the river plume, and (2) fine sediment and particulate metals transported by waves and currents. The transport by the river plume was studied in the NESP Round 2 project. The transport of sediment and particulate metals has never been studied before and is the focus of this model study. The existing SLIM oceanography model of Torres Strait will be used together with the SLIM sediment dynamics model described in Lambrechts et al. (2010)[1]. Field data are available from Wolanski’s 1990s studies in Torres Strait and where possible, new data collected in this phase of the project.

Team: Eric Wolanski, JCU with in-kind support from Professor Eric Deleersnijder and Dr. Jonathan Lambrechts from the University of Louvain, Belgium, and Dr Yanfang Li from the Yantai Institute for Coastal Zone Research, Chinese Academy of Sciences.

Major tasks:

  1. Extend the existing SLIM / MOHID hydrodynamic model for the Torres Strait region to include capability to model sediment (and particulate metal) transport from the Fly River.
  2. Assess the model results in the context of the field data and remote sensing information where possible.
  3. Prepare a report of the findings including key limitations.

Analysis of trace metals in seagrass leaves: Purpose- To assess the ecological relevance of trace metal concentrations in seagrass, an important food source for the highly valued turtle and dugong populations in the region, by analysing trace metals in seagrass leaves at sites around Saibai, Boigu and near the Warrior Reefs.

Team: Jon Brodie, JCU; with in-kind support from Katherine Dafforn, Macquarie University

Major tasks:

  1. In collaboration with the field campaigns for trace metal analysis in sediment and water column (where possible), undertake 2 collections of seagrass leaves for trace metal analysis: 1) end of monsoon (around March 2019) and end of south east trade wind season (around September 2019). Sampling will cover 12 sites (replicates) including 6 along the western PNG coast near Boigu, Saibai and the Warrior Reefs and 6 locations within the islands and further south (about 40km south of coast), beyond the area of predicted influence. Allocation is provided for contribution to vessel expenses for the Warrior Reef sampling if required.
  2. Analyse and report on the findings in the context of the other findings of this study, previous assessments in the Torres Strait region and relevant literature.

Trace metals analysis to be conducted by CSIRO Lucas Heights (a NATA accredited laboratory).

What does it all mean? Combined interpretation of the findings including risk assessment to ecosystems and communities: Purpose – To assess the overall implications of the results of the exposure of sediments and trace metals to ecosystems in the northern Torres Strait, and the probable sources. This will include a qualitative assessment of the potential implications of the findings for the local community.

Team: Jane Waterhouse, Caroline Petus, Jon Brodie, Eric Wolanski, Dieter Tracey, JCU; Simon Apte, CSIRO; Scott Bainbridge, AIMS

Major tasks:

  1. Undertake a semi-quantitative risk assessment of the combined results of all components of this study to draw conclusions regarding the potential influence of the Fly River on the northern Torres Strait.
  2. Explore scenarios of the potential implications of changes to the operation of Ok Tedi mine in the future (e.g. extended mine life).
  3. Generate synthesis products for different audiences to summarise the overall project outputs (including results from NESP Projects 2.2.1 and 2.2.2 since 2016).
  4. Work with key stakeholders to communicate the findings of the studies.

The project will involve close collaboration with the TSRA who are involved in the proposed research, as well as the major end users (see below).

Link to other NESP projects

There are no other current NESP projects in the Torres Strait region. Work conducted as part of NESP Project 3.3.3 will be considered in the interpretation of the results if relevant. The project team will also liaise with Project 2.5.1 (lead by Dr Stephen Lewis) to determine if any of the sediment tracing techniques applied in that project are applicable to this study.

Outside of the NESP, we have worked closely with the WWF Rivers to Reefs to Turtles project by sharing information on metal concentrations in seagrass from the Torres Strait (provided by Dr Katherine Dafforn in this project) and WWF project results from the Howick Island group (undisturbed area in the Great Barrier Reef), Cleveland Bay and Upstart Bay.


  • Locations within the Torres Strait assessed in NESP Projects 2.2.1 and 2.2.2 to be outside of the influence of the Fly River in the work to date.

Summary of how it is expected that the research will be applied to inform decision-making and on-ground action.

The project will deliver:

  1. Additional evidence to document the extent and frequency of the influence of Fly River runoff on highly diverse marine ecosystems in the Torres Strait, to guide the Australian Government in assessing the relative risk of catchment activities in neighbouring countries to Australia’s natural and cultural assets.
  2. Synopsis of the estimated spatial extent Fly River discharge intrudes into the northern Torres Strait, the temporal patterns of discharge, and the plume constituents to inform regional management and planning initiatives, and local communities of the influence of Fly River discharges on northern Torres Strait ecosystems.
  3. Expansion of previous ocean monitoring to provide a longer term record of ocean conditions including provision of real-time weather data to local communities.

The results will also provide a useful contribution to TSRA regional reporting.[2]

Specific management or policy outcomes

  • TSRA and the Australian Government will be able to utilise the results of these studies to ascertain whether or not there are potential ongoing and potentially increasing threats to Torres Strait ecosystems, and therefore, whether to commission further investigations into impacts on ecosystem health, and where to target management effort or international interactions.
  • Supporting information can be used by TSRA for the design of an ongoing integrated Torres Strait monitoring program.
  • The results will guide TSRA in the allocation of monitoring and management resources to high-risk pressures and locations in the Torres Strait region.

The results will provide guidance to the Great Barrier Reef Marine Park Authority on the potential threats to important species including turtle and dugong that rely on the valuable seagrass habitats of the Torres Strait region and transit the Great Barrier Reef

[1] Lambrechts et al. (2010); The importance of wave-induced bed fluidisation in the fine sediment budget of Cleveland Bay, Great Barrier Reef. Estuarine, Coastal and Shelf Science 89, 154-162).

[2] e.g. Torres Strait State of the Environment Report and Torres Strait Land and Sea Management Strategy.


NESP 2017 Research Priority Alignment

The project aligns with Theme 1 and Theme 2 of the NESP Research Priorities:

  • Theme 1: Improved understanding of the impacts, including cumulative impacts, and pressures on priority freshwater, coastal and marine ecosystems and species.
  • Theme 2: Maximise the resilience of vulnerable species to the impacts of climate change and climate variability by reducing other pressures, including poor water quality project directly delivers data and knowledge to end users on the impacts of land use change on coastal wetlands, and how projects aimed at restoring and repairing wetlands achieve the objectives.  This project includes a large range of end users that are involved in projects from day one, and continually assist with generation of data and information.  This NESP project, like our previous projects, will continually promote the results and achievements made by project partners.


Project Keywords

Torres Strait; Fly River discharge; Water quality; Ecosystem health; Metal contamination.


Project Funding

This project is jointly funded through JCU, CSIRO, AIMS and the Australian Government’s National Environmental Science Program.