This dataset summarises intertidal benthic surveys of Dungeness Reef, Torres Strait in February 2021 into 3 GIS shapefiles. (1) The site shapefile describes (a) seagrass presence/absence and (b) species composition at 128 sites. (2) The meadow shapefile describes seagrass communities for the reef-top meadow. (3) The interpolation shapefile describes variation in seagrass biomass across sites in the meadow. This project is part of ongoing long-term monitoring of intertidal reef-top seagrass in Torres Strait. This data describes seagrass at the Dungeness Reef intertidal reef-top meadow in 2021. The reef has been surveyed annually since 2016. This monitoring provides essential information to the TSRA, Australian and Queensland governments for dugong and turtle management plans, complimenting dugong and turtle research studies in the region. The sampling methods used to study, describe and monitors seagrass meadows were developed by the TropWATER Seagrass Group and tailored to the location and habitat surveyed; these are described in detail in the relevant publications (https://research.jcu.edu.au/tropwater). 1 Location Sites were surveyed by helicopter. At each site latitude and longitude was recorded by GPS. Sediment type was recorded. 2 Seagrass metrics At each site observers estimated the percent cover of seagrass, then for three quadrats within each site, ranked seagrass biomass and estimated the percent contribution of each species to that biomass. Helicopter was used for the intertidal surveys following TropWATER’s methods to assess areas at high risk from shipping accidents in Torres Strait (Carter et al. 2013). At each site the helicopter comes into a low hover and seagrass was ranked and species composition estimated from three 0.25 m2 quadrats placed randomly within a 10m2 circular area. Seagrass above-ground biomass was determined using the “visual estimates of biomass” technique (Mellors 1991) using trained observers. This involves ranking seagrass biomass while referring to a series of quadrat photographs of similar seagrass habitats for which the above-ground biomass has been previously measured. Three separate biomass scales are used: low biomass, high biomass, and Enhalus biomass. The percent contribution of each seagrass species to total above-ground biomass within each quadrat is also recorded. At the completion of sampling each observer ranks a series of calibration quadrats. A linear regression is then calculated for the relationship between the observer ranks and the harvested values. This regression is used to calibrate above-ground biomass estimates for all ranks made by that observer during the survey. Biomass ranks are then converted to above-ground biomass in grams dry weight per square metre (g DW m-2). 3 Benthic macro-invertebrates At each site a visual estimate of benthic macro-invertebrate (BMI) percent cover was recorded each site according to four broad taxonomic groups: • Hard coral – All scleractinian corals including massive, branching, tabular, digitate and mushroom. • Soft coral – All alcyonarian corals, i.e. corals lacking a hard limestone skeleton. • Sponge. • Other BMI – Any other BMI identified, e.g. hydroid, ascidian, barnacle, oyster, mollusc. Other BMI are listed in the “comments” column of the GIS site layer. 4 Algae A visual estimate of algae percent cover was recorded at each site. When present, algae were categorised into five functional groups and the percent contribution of each functional group was estimated: • Erect macrophyte – Macrophytic algae with an erect growth form and high level of cellular differentiation, e.g. Sargassum, Caulerpa and Galaxaura species. • Erect calcareous – Algae with erect growth form and high level of cellular differentiation containing calcified segments, e.g. Halimeda species. • Filamentous – Thin, thread-like algae with little cellular differentiation. • Encrusting – Algae that grows in sheet-like form attached to the substrate or benthos, e.g.

This dataset summarises intertidal benthic surveys of Dungeness Reef, Torres Strait, in February 2019 into 3 GIS shapefiles. The site shapefile describes (1) seagrass presence/absence and (2) species composition at 92 sites. The meadow shapefile describes seagrass community for the reef-top meadow. The interpolation shapefile describes variation in seagrass biomass across sites for the meadow. This project is part of ongoing long-term monitoring of intertidal reef-top seagrass in Torres Strait. This data describes seagrass at the Dungeness Reef intertidal reef-top meadow in 2019. The reef has been surveyed annually since 2016. This monitoring provides essential information to the TSRA, Australian and Queensland governments for dugong and turtle management plans, complimenting dugong and turtle research studies in the region. Methods: The sampling methods used to study, describe and monitors seagrass meadows were developed by the TropWATER Seagrass Group and tailored to the location and habitat surveyed; these are described in detail in the relevant publications (https://research.jcu.edu.au/tropwater). 1 Location Sites were surveyed by helicopter. At each site latitude and longitude was recorded by GPS. Sediment type was recorded. 2 Seagrass metrics At each site observers estimated the percent cover of seagrass, then for three quadrats within each site, ranked seagrass biomass and estimated the percent contribution of each species to that biomass. Helicopter was used for the intertidal surveys following TropWATER’s methods to assess areas at high risk from shipping accidents in Torres Strait (Carter et al. 2013). At each site the helicopter comes into a low hover and seagrass was ranked and species composition estimated from three 0.25 m2 quadrats placed randomly within a 10m2 circular area. Seagrass above-ground biomass was determined using the “visual estimates of biomass” technique (Mellors 1991) using trained observers. This involves ranking seagrass biomass while referring to a series of quadrat photographs of similar seagrass habitats for which the above-ground biomass has been previously measured. Three separate biomass scales are used: low biomass, high biomass, and Enhalus biomass. The percent contribution of each seagrass species to total above-ground biomass within each quadrat is also recorded. At the completion of sampling each observer ranks a series of calibration quadrats. A linear regression is then calculated for the relationship between the observer ranks and the harvested values. This regression is used to calibrate above-ground biomass estimates for all ranks made by that observer during the survey. Biomass ranks are then converted to above-ground biomass in grams dry weight per square metre (g DW m-2). 3 Benthic macro-invertebrates At each site a visual estimate of benthic macro-invertebrate (BMI) percent cover was recorded each site according to four broad taxonomic groups: • Hard coral – All scleractinian corals including massive, branching, tabular, digitate and mushroom. • Soft coral – All alcyonarian corals, i.e. corals lacking a hard limestone skeleton. • Sponge. • Other BMI – Any other BMI identified, e.g. hydroid, ascidian, barnacle, oyster, mollusc. Other BMI are listed in the “comments” column of the GIS site layer. 4 Algae A visual estimate of algae percent cover was recorded at each site. When present, algae were categorised into five functional groups and the percent contribution of each functional group was estimated: • Erect macrophyte – Macrophytic algae with an erect growth form and high level of cellular differentiation, e.g. Sargassum, Caulerpa and Galaxaura species. • Erect calcareous – Algae with erect growth form and high level of cellular differentiation containing calcified segments, e.g. Halimeda species. • Filamentous – Thin, thread-like algae with little cellular differentiation. • Encrusting – Algae that grows in sheet-like form attached to the substrate or benthos, e.g.

This dataset summarises intertidal benthic surveys of Dungeness Reef, Torres Strait, in February 2020 into 3 GIS shapefiles. The site shapefile describes (1) seagrass presence/absence and (2) species composition at 92 sites. The meadow shapefile describes seagrass community for the reef-top meadow. The interpolation shapefile describes variation in seagrass biomass across sites for the meadow. This project is part of ongoing long-term monitoring of intertidal reef-top seagrass in Torres Strait. This data describes seagrass at the Dungeness Reef intertidal reef-top meadow in 2020. The reef has been surveyed annually since 2016. This monitoring provides essential information to the TSRA, Australian and Queensland governments for dugong and turtle management plans, complimenting dugong and turtle research studies in the region. Methods: The sampling methods used to study, describe and monitors seagrass meadows were developed by the TropWATER Seagrass Group and tailored to the location and habitat surveyed; these are described in detail in the relevant publications (https://research.jcu.edu.au/tropwater). 1 Location Sites were surveyed by helicopter. At each site latitude and longitude was recorded by GPS. Sediment type was recorded. 2 Seagrass metrics At each site observers estimated the percent cover of seagrass, then for three quadrats within each site, ranked seagrass biomass and estimated the percent contribution of each species to that biomass. Helicopter was used for the intertidal surveys following TropWATER’s methods to assess areas at high risk from shipping accidents in Torres Strait (Carter et al. 2013). At each site the helicopter comes into a low hover and seagrass was ranked and species composition estimated from three 0.25 m2 quadrats placed randomly within a 10m2 circular area. Seagrass above-ground biomass was determined using the “visual estimates of biomass” technique (Mellors 1991) using trained observers. This involves ranking seagrass biomass while referring to a series of quadrat photographs of similar seagrass habitats for which the above-ground biomass has been previously measured. Three separate biomass scales are used: low biomass, high biomass, and Enhalus biomass. The percent contribution of each seagrass species to total above-ground biomass within each quadrat is also recorded. At the completion of sampling each observer ranks a series of calibration quadrats. A linear regression is then calculated for the relationship between the observer ranks and the harvested values. This regression is used to calibrate above-ground biomass estimates for all ranks made by that observer during the survey. Biomass ranks are then converted to above-ground biomass in grams dry weight per square metre (g DW m-2). 3 Benthic macro-invertebrates At each site a visual estimate of benthic macro-invertebrate (BMI) percent cover was recorded each site according to four broad taxonomic groups: • Hard coral – All scleractinian corals including massive, branching, tabular, digitate and mushroom. • Soft coral – All alcyonarian corals, i.e. corals lacking a hard limestone skeleton. • Sponge. • Other BMI – Any other BMI identified, e.g. hydroid, ascidian, barnacle, oyster, mollusc. Other BMI are listed in the “comments” column of the GIS site layer. 4 Algae A visual estimate of algae percent cover was recorded at each site. When present, algae were categorised into five functional groups and the percent contribution of each functional group was estimated: • Erect macrophyte – Macrophytic algae with an erect growth form and high level of cellular differentiation, e.g. Sargassum, Caulerpa and Galaxaura species. • Erect calcareous – Algae with erect growth form and high level of cellular differentiation containing calcified segments, e.g. Halimeda species. • Filamentous – Thin, thread-like algae with little cellular differentiation. • Encrusting – Algae that grows in sheet-like form attached to the substrate or benthos, e.g.

This dataset summarises intertidal benthic surveys of Kai and Gariar Reefs (Orman Reefs, Torres Strait) in September 2019 into 3 GIS shapefiles. (1) The site shapefile describes (a) seagrass presence/absence and (b) species composition at 124 sites. (2) The meadow shapefile describes seagrass communities for the two reef-top meadows. (3) The interpolation shapefile describes variation in seagrass biomass across sites for the two reef-top meadows. This project is part of ongoing long-term monitoring of intertidal reef-top seagrass in Torres Strait, and follows on from a baseline survey of Orman Reefs in September 2017. It describes seagrasses at two of the largest reefs in the Orman Reef complex – Kai (Koey Maza) and Gariar Reefs. This monitoring provides essential information to the TSRA, Australian and Queensland governments for dugong and turtle management plans, complimenting dugong and turtle research studies in the region. Methods: The sampling methods used to study, describe and monitors seagrass meadows were developed by the TropWATER Seagrass Group and tailored to the location and habitat surveyed; these are described in detail in the relevant publications (https://research.jcu.edu.au/tropwater). 1 Location Sites were surveyed by helicopter. At each site latitude and longitude was recorded by GPS. Sediment type was recorded. 2 Seagrass metrics At each site observers estimated the percent cover of seagrass, then for three quadrats within each site, ranked seagrass biomass and estimated the percent contribution of each species to that biomass. Helicopter was used for the intertidal surveys following TropWATER’s methods to assess areas at high risk from shipping accidents in Torres Strait (Carter et al. 2013). At each site the helicopter comes into a low hover and seagrass was ranked and species composition estimated from three 0.25 m2 quadrats placed randomly within a 10m2 circular area. Seagrass above-ground biomass was determined using the “visual estimates of biomass” technique (Mellors 1991) using trained observers. This involves ranking seagrass biomass while referring to a series of quadrat photographs of similar seagrass habitats for which the above-ground biomass has been previously measured. Three separate biomass scales are used: low biomass, high biomass, and Enhalus biomass. The percent contribution of each seagrass species to total above-ground biomass within each quadrat is also recorded. At the completion of sampling each observer ranks a series of calibration quadrats. A linear regression is then calculated for the relationship between the observer ranks and the harvested values. This regression is used to calibrate above-ground biomass estimates for all ranks made by that observer during the survey. Biomass ranks are then converted to above-ground biomass in grams dry weight per square metre (g DW m-2). 3 Benthic macro-invertebrates At each site a visual estimate of benthic macro-invertebrate (BMI) percent cover was recorded each site according to four broad taxonomic groups: • Hard coral – All scleractinian corals including massive, branching, tabular, digitate and mushroom. • Soft coral – All alcyonarian corals, i.e. corals lacking a hard limestone skeleton. • Sponge. • Other BMI – Any other BMI identified, e.g. hydroid, ascidian, barnacle, oyster, mollusc. Other BMI are listed in the “comments” column of the GIS site layer. 4 Algae A visual estimate of algae percent cover was recorded at each site. When present, algae were categorised into five functional groups and the percent contribution of each functional group was estimated: • Erect macrophyte – Macrophytic algae with an erect growth form and high level of cellular differentiation, e.g. Sargassum, Caulerpa and Galaxaura species. • Erect calcareous – Algae with erect growth form and high level of cellular differentiation containing calcified segments, e.g. Halimeda species. • Filamentous – Thin, thread-like algae with little cellular

This dataset summarises intertidal benthic surveys of Kai and Gariar Reefs (Orman Reefs, Torres Strait) in November 2018 into 3 GIS shapefiles. (1) The site shapefile describes (a) seagrass presence/absence and (b) species composition at 124 sites. (2) The meadow shapefile describes seagrass communities for the two reef-top meadows. (3) The interpolation shapefile describes variation in seagrass biomass across sites for the two reef-top meadows. This project is part of ongoing long-term monitoring of intertidal reef-top seagrass in Torres Strait, and follows on from a baseline survey of Orman Reefs in September 2017. It describes seagrasses at two of the largest reefs in the Orman Reef complex – Kai (Koey Maza) and Gariar Reefs. This monitoring provides essential information to the TSRA, Australian and Queensland governments for dugong and turtle management plans, complimenting dugong and turtle research studies in the region. Methods: The sampling methods used to study, describe and monitors seagrass meadows were developed by the TropWATER Seagrass Group and tailored to the location and habitat surveyed; these are described in detail in the relevant publications (https://research.jcu.edu.au/tropwater). 1 Location Sites were surveyed by helicopter. At each site latitude and longitude was recorded by GPS. Sediment type was recorded. 2 Seagrass metrics At each site observers estimated the percent cover of seagrass, then for three quadrats within each site, ranked seagrass biomass and estimated the percent contribution of each species to that biomass. Helicopter was used for the intertidal surveys following TropWATER’s methods to assess areas at high risk from shipping accidents in Torres Strait (Carter et al. 2013). At each site the helicopter comes into a low hover and seagrass was ranked and species composition estimated from three 0.25 m2 quadrats placed randomly within a 10m2 circular area. Seagrass above-ground biomass was determined using the “visual estimates of biomass” technique (Mellors 1991) using trained observers. This involves ranking seagrass biomass while referring to a series of quadrat photographs of similar seagrass habitats for which the above-ground biomass has been previously measured. Three separate biomass scales are used: low biomass, high biomass, and Enhalus biomass. The percent contribution of each seagrass species to total above-ground biomass within each quadrat is also recorded. At the completion of sampling each observer ranks a series of calibration quadrats. A linear regression is then calculated for the relationship between the observer ranks and the harvested values. This regression is used to calibrate above-ground biomass estimates for all ranks made by that observer during the survey. Biomass ranks are then converted to above-ground biomass in grams dry weight per square metre (g DW m-2). 3 Benthic macro-invertebrates At each site a visual estimate of benthic macro-invertebrate (BMI) percent cover was recorded each site according to four broad taxonomic groups: • Hard coral – All scleractinian corals including massive, branching, tabular, digitate and mushroom. • Soft coral – All alcyonarian corals, i.e. corals lacking a hard limestone skeleton. • Sponge. • Other BMI – Any other BMI identified, e.g. hydroid, ascidian, barnacle, oyster, mollusc. Other BMI are listed in the “comments” column of the GIS site layer. 4 Algae A visual estimate of algae percent cover was recorded at each site. When present, algae were categorised into five functional groups and the percent contribution of each functional group was estimated: • Erect macrophyte – Macrophytic algae with an erect growth form and high level of cellular differentiation, e.g. Sargassum, Caulerpa and Galaxaura species. • Erect calcareous – Algae with erect growth form and high level of cellular differentiation containing calcified segments, e.g. Halimeda species. • Filamentous – Thin, thread-like algae with little cellular

This dataset summarises 40 years of seagrass data collection (1983-2022) within Torres Strait and the Gulf of Carpentaria into two GIS shapefiles: (1) a point shapefile that includes survey data for 48,612 geolocated sites, and (2) a polygon geopackage describing seagrass at 641 individual or composite meadows. Managing seagrass resources in northern Australia requires adequate baseline information on where seagrass is (presence/absence), the mapped extent of meadows, what species are present, and date of collection. This baseline is particularly important as a reference point against which to compare seagrass loss or change through time. The scale of northern Australia and the remoteness of many seagrass meadows from human populations present a challenge for research and management agencies reporting on the state of seagrass ecological indicators. Broad-scale and repeated surveys/studies of areas are logistically and financially impractical. However seagrass data is being collected through various projects which, although designed for specific reasons, are amenable to collating a picture of the extent and state of the seagrass resource. In this project we compiled seagrass spatial data collected during surveys in Torres Strait and the Gulf of Carpentaria into a standardised form with point-specific and meadow-specific spatial and temporal information. We revisited, evaluated, simplified, standardised, and corrected individual records, including those collected several decades ago by drawing on the knowledge of one of our authors (RG Coles) who led the early seagrass data collection and mapping programs. We also incorporate new data, such as from photo records of an aerial assessment of mangroves in the Gulf of Carpentaria in 2017. This project was funded by the National Environmental Science Programme (NESP) Marine and Coastal Hub and Torres Strait Regional Authority (TSRA) in partnership with the Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), James Cook University. The project follows on from TropWATER’s previous work compiling 35 years of seagrass spatial point data and 30 years of seagrass meadow extent data for the Great Barrier Reef World Heritage Area (GBRWHA) and adjacent estuaries, funded through successive NESP Tropical Water Quality Hub Projects 3.1 (2015-2016) and 5.4 (2018-2020). These data sets are now publicly available through the eAtlas data portal: https://doi.org/10.25909/y1yk-9w85 . In making this data publicly available for management, the authors and data custodians request being contacted and involved in decision making processes that incorporate this data, to ensure its limitations are fully understood. Methods: The data were collected using a variety of survey methods to describe and monitor seagrass sites and meadows. For intertidal sites/meadows, these include walking, observations from helicopters in low hover, and observations from hovercraft when intertidal banks were exposed. For subtidal sites/meadows, methods included free diving, scuba diving, video transects from towed cameras attached to a sled with/without a sled net, video drops with filmed quadrats, trawl and net samples, and van Veen grab samples. These methods were selected and tailored by the data custodians to the location, habitat surveyed, and technology available. Important site and method descriptions and contextual information is contained in the original trip reports and publications for each data set provided in Table 1 of Carter et al. (2022). Geographic Information System (GIS) Mapping data for historic records (1980s) were transcribed from original logged and mapped data based on coastal topography, dead reckoning fixes and RADAR estimations. More recent data (1990’s onwards) is GPS located. All spatial data were converted to shapefiles with the same coordinate system (GDA 1994 Geoscience Australia Lambert), then compiled into a single point shapefile and a single polygon shapefile (seagrass meadows)

This dataset summarises subtidal benthic surveys in Yanyuwa Sea Country into 3 GIS shapefiles. (1) A point (site) shapefile describes seagrass presence/absence at 849 subtidal sites surveyed by vessel. (2) The meadow shapefile describes attributes of 46 subtidal seagrass meadows. (3) The interpolation shapefile describes variation in subtidal seagrass biomass across the seagrass meadows. This project is a partnership between the li-Anthawirriyarra rangers, Charles Darwin University, James Cook University, and Mabunji Aboriginal Resource Indigenous Corporation to map the subtidal habitats of the Yanyuwa Indigenous Protected Area (IPA), an area of profound importance to the Marra and Yanyuwa people and to the marine ecosystem of the Gulf of Carpentaria. Benthic habitat maps of Yanyuwa Country were produced, with a focus on seagrass. This project was funded by the NT Government Aboriginal Ranger Grant Program. The sampling methods used to study, describe and monitor seagrass meadows were developed by TropWATER and tailored to the location and habitat surveyed; these are described in detail in the relevant publications (https://research.jcu.edu.au/tropwater). Geographic Information System (GIS) All survey data were entered into a Geographic Information System (GIS) using ArcGIS 10.8. Rectified colour satellite imagery of Yanyuwa Sea Country (Source: Allen Coral Atlas and ESRI), field notes and aerial photographs taken from the helicopter during surveys were used to identify geographical features, such as reef tops, channels and deep-water drop-offs, to assist in determining seagrass meadow boundaries. Three GIS layers were created to describe spatial features of the region: a site layer, seagrass meadow layer, and a seagrass biomass interpolation layer. Site layer This layer contains information on data collected at assessment sites. This layer includes: 1. Temporal survey details – Survey date; 2. Spatial position - Latitude/longitude; 3. Survey location; 4. Seagrass information including presence/absence of seagrass, above-ground biomass (total and for each species), percent cover of seagrass at each site; 5. Benthic macro-invertebrate information including the percent cover of hard coral, soft coral, sponges and other benthic macro invertebrates (e.g. ascidian, clam) at a site; 6. Algae information including percent cover of algae at a site and percent contribution of algae functional groups to algae cover at a site; 7. Open substrate – the percent cover of the site that had no flora or habitat forming benthic invertebrates present; 8. Dominant sediment type - Sediment type based on grain size visual assessment or deck descriptions. 9. Survey method and vessel; 10. Relevant comments and presence/absence of megafauna and animals of interest (dugong, turtle, dolphin); and 11. Data custodians. Seagrass meadow layer Seagrass presence/absence site data, mapping sites, field notes, and satellite imagery were used to construct meadow boundaries in ArcGIS®. The meadow (polygon) layer provides summary information for all sites within each seagrass meadow, including: 1. Temporal survey details – Survey month and year as individual columns and the survey date (the date range the survey took place); 2. Spatial survey details – Survey location, meadow identification number that identifies the reef name and the meadow number. This allows individual meadows to be compared among years; 3. Survey method; 4. Meadow depth for subtidal meadows; 5. Species presence – a list of the seagrass species in the meadow; 6. Meadow density – Seagrass meadows were classified as light, moderate, dense based on the mean biomass of the dominant species within the meadow. For example, a Thalassia hemprichii dominated meadow would be classed as “light” if the mean meadow biomass was <5 grams dry weight m-2 (g DW m-2), and “dense” if mean meadow biomass was >25 g DW m-2. 7. Meadow community type – Seagrass meadows were classified into community types according to

This dataset summarises benthic surveys in Marra Sea Country, including the Limmen Marine Park (Commonwealth) and Limmen Bight Marine Park (Northern Territory) into 4 GIS shapefiles. (1) A point (site) shapefile describes (a) seagrass presence/absence, (b) seagrass species composition, (c) algae cover and (d) benthic macro-invertebrate cover at n=2018 sites surveyed by small vessel and helicopter. (2) A point (site) shapefile describes deep-water (a) seagrass presence/absence, (b) seagrass species composition, (c) algae cover and (d) benthic macro-invertebrate cover at 54 sites surveyed by benthic towed camera and sled net. (3) The meadow shapefile describes attributes of 69 seagrass meadows. (4) The interpolation shapefile describes variation in seagrass biomass across the seagrass meadows. The full report is: Collier C.J., Carter A., Shepherd L., van de Wetering C., Coles R., Evans S., Barrett D., Willan R.C., Groom R. (2022) Benthic habitats of Marra Sea Country - Gulf of Carpentaria. Centre for Tropical Water & Aquatic Marra land and sea country includes coastal waters in the southern Gulf of Carpentaria in the Northern Territory (NT). The Limmen Marine Park (Commonwealth Government) and the Limmen Bight Marine Park (NT Government) are in Marra country. The co-management aspirations identified within the two Marine Park Plans of Management and the Marra Healthy Country Plan include a need to improve information on habitats and key species because they have not been previously mapped. Methods: The sampling methods used to study, describe and monitor seagrass meadows were developed by the TropWATER Seagrass Group and tailored to the location and habitat surveyed; these are described in detail in the relevant publications (https://research.jcu.edu.au/tropwater). Geographic Information System (GIS) All survey data were entered into a Geographic Information System (GIS) developed for Torres Strait using ArcGIS 10.8. Rectified colour satellite imagery of Limmen Bight (Source: Allen Coral Atlas and ESRI), field notes and aerial photographs taken from the helicopter during surveys were used to identify geographical features, such as reef tops, channels and deep-water drop-offs, to assist in determining seagrass meadow boundaries. Four GIS layers were created to describe spatial features of the region: a site layer, seagrass meadow layer, and seagrass biomass interpolation layer. Seagrass site layers Two layers were produced because of additional columns/details on benthic invertebrates that are included in the deep-water shapefile. These layers contains information on data collected at assessment sites and includes: 1. Temporal survey details – Survey date; 2. Spatial position - Latitude/longitude; 3. Survey location; 4. Seagrass information including presence/absence of seagrass, above-ground biomass (total and for each species), percent cover of seagrass at each site and whether individual species were present/absent at a site; 5. Benthic macro-invertebrate information including the percent cover of hard coral, soft coral, sponges and other benthic macro invertebrates (e.g. ascidian, clam) at a site; 6. Algae information including percent cover of algae at a site and percent contribution of algae functional groups to algae cover at a site; 7. Open substrate – the percent cover of the site that had no flora or habitat forming benthic invertebrates present; 8. Dominant sediment type - Sediment type based on grain size visual assessment or deck descriptions. 9. Survey method and vessel 10. Relevant comments and presence/absence of megafauna and animals of interest (sea cucumber, dugong, turtle, dolphin, evidence of dugong feeding trails); 11. Data custodians. Seagrass meadow layer Seagrass presence/absence site data, mapping sites, field notes, and satellite imagery were used to construct meadow boundaries in ArcGIS®. The meadow (polygon) layer provides summary information for all sites within each seagrass meadow, including: 1.

The data set comprises 4 spreadsheets containing trace metal concentrations measured in waters benthic, suspended sediments and seagrasses collected across the Torres Strait during the NESP TWQ 5.14 project. Details of the sampling locations (including coordinates), general chemical and physical parameters and laboratory quality control data are provided. The seagrass data set is also supported by historical data from previous studies: Dight, I.J., Gladstone, W. (1993). Torres Strait baseline study: pilot study final report June 1993. Great Barrier Reef Marine Park Authority Research Publication No. 29. Townsville, Great Barrier Reef Marine Park Authority and Waterhouse, J., Petus, C., Bainbridge, S., Birrer, S.C., Brodie, J., Chariton, A.C., Dafforn, K.A., Johnson, J.E., Johnston, E.L., Li, Y., Lough, J., Martins, F., O’Brien, D., Tracey, D., Wolanski, E., (2018). Identifying the water quality and ecosystem health threats to the Torres Strait and Far Northern Great Barrier Reef arising from runoff of the Fly River. Report to the National Environmental Science Programme. Reef and Rainforest Research Centre Limited, Cairns, 157 pages. The overall aim of the project is to identify the fate of waters from the Fly River in Papua New Guinea and their potential impact on the Torres Strait region. These data sets are metal concentrations in waters, sediments, and seagrasses from locations in the Torres Strait. Some background knowledge of environmental chemistry and water quality management in Australia is needed to properly interpret this data. Methods: Full details of sample collection, chemical analysis, and data processing are provided in the NESP report: Waterhouse, J., Apte, S.C., Petus, C., Angel, B.M., Wolanski, E., Bainbridge, S., Tracey, D., Jarolimek, C.V., King, J., Mellors, J., Brodie, J., (2021). NESP Project 5.14. Assessing the influence of the Fly River discharge on the Torres Strait. Report to the National Environmental Science Programme. Reef and Rainforest Research Centre Limited, Cairns. In brief: Water samples were collected at locations around Boigu and Saibai (see maps in spreadsheets for details). Sediment cores were collected using a gravity corer at locations detailed in the spreadsheets and sectioned in the field. The samples were frozen and transported to CSIRO Lucas Heights for analysis. Seagrass samples were either, taken by hand or seagrass rake (5 replicates), transferred to ziplock plastic bags and stored frozen and then transported to the CSIRO Lucas Heights Laboratory for trace metal analysis. Water samples were filtered, metals extracted and determined by inductively coupled plasma mass spectrometry. Sediment samples were digested in mixed acids using microwave assisted dissolution and determined by inductively coupled plasma mass spectrometry. Sediment was rinsed from the seagrass leaves with Milli-Q® water before a minimum of 200 mg of seagrass was weighed for each sample. The seagrass was then freeze dried using a Christ Alpha 1-2 LD Freeze Dryer. The dried seagrass samples were digested by high pressure/temperature nitric acid microwave digestion using a CEM MARS6 Microwave (in-house Method C-225). Metals were quantified by Inductively coupled plasma mass spectrometry (ICP-MS) using an Agilent 8800 ICP-MS (in-house method C-209). The certified reference material BCR-279 (Sea Lettuce, Ulva Lactua) was digested and analysed with the samples as a check on accuracy. Limitations of the data: The data provided presents a snapshot of water, sediment and seagrass quality at locations in the Torres Strait. It is not a comprehensive data set in terms of spatial and temporal coverage. Guidelines have not yet been developed to identify environmentally acceptable ranges of trace element concentrations for seagrass. Many factors can affect metal concentrations measured. Factors can include sampling intensity, timing of sampling, analytical procedures; relative concentration of other metals in the plant and

This dataset summarises benthic habitat and fish surveys in West Cape York, including the West Cape York Marine Park (Commonwealth), southern Dugong Sanctuary, Angkamuthi and Kaurareg Sea Country into 2 GIS shapefiles. (1) A point (site) shapefile showing point location of 407 habitat survey sites. (2) A point (site) shapefile showing point location of BRUV (baited remote underwater video) deployments to survey fish at 42 sites. The full report is: Carter A, Groom R, Smith T, Shepherd L, van de Wetering C and Willan R (2023). Benthic habitats, fish and invertebrate communities of West Cape York Marine Park and surrounding waters. Centre for Tropical Water & Aquatic Ecosystem Research (TropWATER) Report Number 23/31, James Cook University, Cairns, pp.90 The West Cape York Marine Park (WCYMP), Queensland, is one of eight marine parks in the North Network of Australian Marine Parks. The eastern section of the WCYMP, southern part of the Torres Strait Dugong Sanctuary, and adjacent coastal waters were surveyed December 3‒16 2021, on board the MV Eclipse. The survey was a collaboration between researchers from TropWATER (James Cook University), Charles Darwin University/Australian Institute of Marine Science, Torres Strait Regional Authority, Kaurareg Native Title Aboriginal Corporation representing Kaurareg rangers and Traditional Owners, and Ipima Ikaya Aboriginal Corporation representing Angkamuthi and Gudang Yadhaykenu Traditional Owners. This work was undertaken for, and funded by, the Director of National Parks (Australian Government) and Torres Strait Regional Authority. The objectives of the survey were to: (1) Collaborate with Traditional Owners and Indigenous rangers to share knowledge and better understand sea country resources and inform management responses; (2) identify any changes/trends in the extent, health and diversity of seagrass meadows; (3) provide information to better understand the key pressures on the health of seagrass meadows and the culturally and socially significant species which they support; (4) record invertebrate diversity; (5) provide habitat maps for the survey area; and (6) conduct a pilot study of fish communities. The sampling methods used to survey benthic habitats were developed by TropWATER and are tailored to the location and habitat surveyed; these are described in detail in the relevant publications (https://research.jcu.edu.au/tropwater). Geographic Information System (GIS) All survey data were entered into a Geographic Information System (GIS) using ArcGIS 10.8. Two GIS layers were created to describe spatial features of the region: a habitat site layer and a fish site layer. Habitat site layer This layer contains information on the location and survey details for habitat assessment sites, and includes: 1. Temporal survey details – Survey date; 2. Spatial position - Latitude/longitude; 3. Survey location; 4. Site depth; 5. Survey method and vessel; 6. Vessel; 7. Data author and custodians. Fish site layer This layer contains information on the location and survey details for fish survey sites, and includes baited remote underwater video stations (BRUVS) at fish survey sites, and includes: 1. Temporal survey details – Survey date; 2. Spatial position - Latitude/longitude; 3. Survey location; 4. Site depth; 5. Survey method and vessel; 6. Vessel; 7. Data author and custodians. Base map The base map used is courtesy ESRI 2022. Format of the data This dataset consists of a 2 point layer packages with a geographic coordinate system of GDA2020: 1. West Cape York habitat sites 2021.lpk - Symbology representing point location of each habitat survey site 2. West Cape York fish sites 2021.lpk- Symbology representing point location of each fish survey site where baited remote underwater video stations (BRUVS) were deployed Data Dictionary West Cape York habitat sites 2021 (point data) LATITUDE (numeric) – Site location in decimal degrees south LONGITUDE (numeric) – Site location in decimal