Australian Tropical Reef Features - Boundaries of coral and rocky reefs (NESP MaC 3.17, AIMS)

Full description

This dataset contains a shapefile of the boundaries of more than 20,000 tropical coral reefs, rocky reefs and sand banks of tropical Australia, covering Indian Ocean, Timor Sea, Gulf of Carpentaria, Torres Strait, Great Barrier Reef and the Coral Sea. This dataset provides the first comprehensive mapping of the reefs of tropical Australia, covering intertidal rocky reefs through to offshore oceanic coral reefs. It includes all reefs shallower than approximately 30 m on the continental shelf and up to 60 m depth in oceanic waters. It is intended to support national environmental accounting, national habitat mapping, creating reef maps, marine science planning, marine park planning, mapping of sea country for traditional owner groups and identifying important marine habitat that should be considered in environmental impact assessments.

This dataset is made from the integration of coral reef mapping datasets developed for different regions (GBR, Torres Strait, Coral Sea and Northern and Western Australia) into a single national-scale dataset. It contains 21,832 mapped features. The features are classified according to the Reef Boundary Type classification, and cross walked to the Natural Values Common Language (NVCL) and Seamap Australia Classification scheme. Some features outside the Australian Exclusive Economic Zone (EEZ) are included. Sovereignty of each reef is assigned to allow easy filtering to exclude reefs outside of Australia. The bathymetry statistics (10th, 50th and 90th percentile) of each reef are calculated from the Multi-resolution bathymetry composite surface for Australian waters (EEZ) (Flukes, 2024) and AusBathyTopo (Australia) 250m 2024 (Geoscience Australia, 2024) datasets.

Features in the Coral Sea, Torres Strait and North and West Australia are mapped at a spatial scale of 1:250,000, with a 90th percentile boundary error of approximately 100 m. Features in the GBR Marine Park are less accurate because they are based on older mapping, with typical 90th percentile boundary errors of approximately 300 m, though in some cases boundary errors exceed 1 km.

In this dataset we standardise attributes across datasets, and for the GBR we apply corrections to the input source mapping. The GBR marine park mapping is originally based on the GBRMPA GBR Features indicative reef boundaries datasets. We apply corrections to the feature classifications, remove false positive reefs and add reefs missing from the original dataset.

Analysis considerations:

This dataset provides the outer boundary of coral reef habitats and thus includes multiple habitats within coral reefs such as reef slope, reef crest and reef flats. For the Northern and Western Australia coral reefs are represented by both the 'active' portion of the reef (RB_Type_L3 = 'Coral Reef') and the dormant geological reef flat that is largely covered in sand (RB_Type_L3 = 'Coral Reef Flat'). In some high tidal range conditions in Western Australia and Northern Territory, reefs have grown above the mean tidal level. These are recorded as 'High Intertidal Coral Reef' and are often surrounded by, or adjacent to, deeper, more conventional reefs. If the analysis requires the full geological extent of reefs, these sub-reef types should be dissolved together. This can be achieved by using Level 2 of the Reef Boundary Type classification, in which all of these types are considered coral reefs.

The depth category (DepthCat) of each feature provides an indication of the depth of the shallowest portion (10 percent) of the feature. In many cases in the Coral Sea and in Northern and Western Australia, the depth category was determined from satellite imagery. This approach was used to ensure consistent classification across the large study area where the resolution of available bathymetry datasets was insufficient to resolve the heights of small reef features. Because the depth category is based on the top portion of the feature, there may be a significant proportion that is substantially deeper than the assigned classification. This reflects the limitation of assigning a single depth class to large reef features.

Where depth categories were not assigned in the source datasets (Torres Strait, GBR and approximately 30 percent of the Northern and Western Australia features), the depth category of features was estimated using two datasets. For reefs inside the Australian Exclusive Economic Zone (EEZ), the 'Multi-resolution bathymetry composite surface for Australian waters (EEZ)' (Flukes, 2024) was used. For reefs outside the EEZ, the AusBathyTopo (Australia) 250 m 2024 (Geoscience Australia, 2024) bathymetry was used. The validity of bathymetry estimates from digital elevation models is highly variable and depends on the detail of the source bathymetry. Estimating the depth of the tops of small reef features is very sensitive to the resolution of the source DEM, with errors of 5 - 20 m or more being common.

In the Coral Sea, we incorporated both the Atoll Platforms dataset and the Reefs and Cays dataset so that these large oceanic structures were represented. These 'Atoll Platform' features were mapped as 'Oceanic Platform' in the Reef Boundary Type classification and 'Oceanic unvegetated sediments' in the NVCL. This can be partly misleading because it implies that these areas are unvegetated; however, significant proportions of lagoonal areas are covered in vegetation. If this distinction is important for your analysis, the vegetated areas have been mapped separately in the Coral Sea Oceanic Vegetation dataset (Lawrey, 2024).

Methods:
The complete dataset can be regenerated from scratch by cloning the companion Git repository and executing scripts 01 to 06 sequentially. These scripts automate the downloading of third-party inputs, application of manual overrides, normalisation of attributes, merging of regional layers, estimation of sovereignty, derivation of depth classes, and cross-walking to the Natural Values Common Language. Because every manual correction is stored as an external shapefile and no interactive editing is required, the workflow is completely reproducible.

Step 1 - acquire inputs (01-download-input-data.py)
The script fetches the four regional reef boundary layers, the 2024 EEZ land union shapefile and the two bathymetry mosaics.

Step 2 – patch, standardise and merge regional datasets
Three patch scripts prepare the source layers to a common schema for merging. The most significant modification was for the Torres Strait and the GBR where manually drawn edits were applied to the source dataset. A point shapefile was used to indicate edit commands (move, reshape, merge, remove, and classification adjustments) and a polygon shapefile used to supply the corrected outlines or to add previously unmapped reefs. The North and West Australian Reef Features was already aligned with the dataset schema and the only modification needed was to trim unused attributes. For the Coral Sea, Atoll Platforms are represented as a separate dataset to the reef boundaries. The Atoll Platforms features were incorporated into the dataset by cookie cutting the Coral Sea reef boundaries to create features that represent the lagoonal floor of the atolls in the Coral Sea. After these operations all three sources share the same schema and were then merged into a single shapefile for subsequent processing.

Step 3 – assign sovereignty
The country associated with feature was assigned using the Union of the ESRI Country shapefile and the Exclusive Economic Zones layer. This was to allow convenient filtering of features to the Australian EEZ. The attribution is supplied for research convenience and is not an official statement of maritime boundaries.

Step 4 – derive bathymetry statistics and depth classes
This step involves ensuring all features are assigned a depth category, as this is needed for assigning shallow or mesophotic classification in the Natural Values Common Language. Where the source dataset does not have a DepthCat assigned one is derived from the Multi-resolution bathymetry composite surface for Australian waters (EEZ) (Flukes, 2024) and the AusBathyTopo 250m 2024 (Geoscience Australia, 2024) datasets. As part of this processing the 10th, 50th and 90th percentile depths (DEM10p, DEM50p, DEM90p) is estimated for each feature.

Step 5 – cross-walk to external classification schemes
A crosswalk lookup table is used to translates each feature into Natural Values Common Language and Seamap Australia classifications. Features that fail to match this table are flagged for review. This final step also recalculates the feature areas (Area_km2) and compacts the size of the text attributes to make the shapefile as small as possible.


Dataset versions:

This dataset will be progressively improved over time as improvements to the source datasets become available.

Version v0-1 - Initial release (5 Aug 2025):

This initial version is intended for use in the updated Natural Values Ecosystems (2022) dataset https://seamapaustralia.org/map/#066e7a74-7378-45aa-b10a-564304aaa6f7 for NESP MaC 4.20. All features have been visually reviewed against satellite imagery, but no additional in-depth validation has been applied.

This version uses v0-4 of the North and West Australian Features dataset. That version was based solely on remote sensing for mapping and classification. Comparison with bathymetry and marine chart datasets was intentionally withheld so they could be used for validation. Version v0-4 focused on digitising coral reefs first, then rocky reefs, and finally sediment features. As a result, some sediment-based feature types are significantly under-represented. There are probably hundreds of sand banks missing, and only a few features in the 'Seagrass' classification types 'Seagrass on Sediment' and 'Seagrass on Coral Reef' have been mapped. The mapping of seagrass is incomplete and should not be used. In the Pilbara there are many limestone reefs that are difficult to distinguish from modern coral reefs. In some cases modern coral reefs partly cover ancient limestone reefs. As a result, there are likely to be significant classification inaccuracies in this region, with limestone reefs incorrectly classified as coral reefs, and portions of coral reefs over limestone reefs not separated.

The DepthCat attribute values in this version should be considered draft quality only. For the North and West Australian Tropical Reefs dataset, DepthCat was evaluated and set for only 70 percent of features, and no quality control or accuracy assessment was performed on these classifications due to project time constraints. The primary focus was on setting depth classifications that would affect the Natural Values Common Language classification.

The greatest source of error in version v0-1 is in the source dataset for the GBR Marine Park. This portion of the mapping is based on the 2008 GBRMPA GBR Features dataset that was integrated into the Complete GBR composite dataset (Lawrey and Stewart, 2016). Boundary errors of over 1 km are common for larger reefs, deep reefs are under-represented, and inshore reef boundaries typically overlap only about 50 percent of their true extent. To improve this dataset prior to integration, we applied nearly 1,000 fixes. These included 93 classification corrections, the removal of 144 false reefs, boundary improvements to 255 reefs, and the addition of 791 previously unmapped reefs. While these are quite a few corrections, most (>90 percent) existing features need redrawing to achieve accuracy similar to the other regions. Edits to the GBR Features were performed manually using Sentinel-2 All-Tide composite imagery (Hammerton and Lawrey, 2024). Given the limited time available for corrections (10 hours of digitisation), the main focus was removing false reefs and correcting the classification of reefs into rocky reefs, coral reefs and sand banks. In this regard the corrections are relatively comprehensive.

The University of Queensland recently remapped the GBR under the project 'Delivery of a 3D Live Habitat Map for the Full Extent of the Great Barrier Reef (Phase Two)' for GBRMPA. It is under review as of April 2025. We intended to switch to using this updated mapping when this dataset is available.

This version uses the v1 of the Coral Sea Features dataset which was published in 2025. No improvements were made to this dataset.

Errata The 'Cay' features were removed from the Torres Strait and GBR datasets because they were treated as islands during processing. This is inconsistent with the Coral Sea mapping, where cays were included. Future version will include cays in the GBR.
A review of the depth categories indicate that there are approximately 50 - 80 fringing coral reefs in the Kimberley that have been marked incorrectly with DepthCat='Shallow' when they should be 'Very Shallow'.

Format:
- AU_NESP-MaC-3-17_AIMS_NW-Aus-Features.shp (Shapefile, 51 MB, 21,832 features)


Data dictionary:

- RB_Type_L3 (String): Reef Boundary Type Classification Level 3 - Most detailed classification applied to features. See
- Attachment (String): Attachment classification of the feature to islands and mainland. Values: 'Fringing', 'Isolated', 'Land' and 'Oceanic'
- DepthCat (String): Depth of the top 90th percentile of the feature. 'Land': Islands, 'Surface': Floating man made structures, 'Intertidal', 'Very Shallow': Shallower than -2.5 m LAT, 'Shallow', -30 m MSL to -2.5 m LAT, 'Deep', < -30 m MSL.
- DepthCatSr (String): Source of information used to estimate the depth category.
- FeatConf (String): Confidence that the mapped feature is a feature of interest and not an artefact.
- TypeConf (String): Confidence that the RB_Type_L3 classification is correct.
- EdgeSrc (String): Source of information used to primarily digitise the feature boundary.
- EdgeAcc_m (Integer): Estimated error in the digitisation of the feature boundary in metres from the true boundary for 90th percentile of digitised points.
- ReefID (String): Unique persistent identifier assigned to the feature. This is assigned for features from TS-GBR Features or Coral Sea Features datasets. No IDs have been assign for North and West Australian features yet.
- Dataset: (String) Title of the source dataset.
- OrigType (String): Feature type of the original dataset
This is the feature original classification from the source dataset
- Sovereign1 (String): Primary country with the most reef area.
- Sovereign2 (String): Secondary country with the lesser reef area (if applicable). NULL if the reef only occurs in one country.
- Sov1_Perc (Integer): Percentage of reef area in the primary country
- Sov2_Perc (Integer): Percentage of reef area in the secondary country (if applicable)
- Union (String): Country or treaty designation, concatenated with semicolons for cross-boundary reefs
- DEM10p (Float): 10th percentile of the depths within the feature polygon, based on DEM specified in DEMSr.
- DEM50p (Float): 50th percentile of the depths within the feature polygon, based on DEM specified in DEMSr.
- DEM90p (Float): 90th percentile of the depths within the feature polygon, based on DEM specified in DEMSr.
- DEMSr (String): Source of the Digital Elevation Model used to estimate the DEM percentiles for the feature.
- RB_Type_L2 (String): Level 2 classification of the Reef Boundary Type Classification. This groups all the different coral reef types to a 'Coral Reef' class, and the different rocky reef types to a 'Rocky Reef' class.
- RB_Type_L1 (String): Level 1 classification of the Reef Boundary Type Classification. The lowest detailed level of classification. It primarily distinguished between 'Reefs', all features with hard substrates, 'Sediment', soft sediment areas, and 'Land'.
- NvclEco: (String) Natural Values Common Language classification Ecosystem classification. This is a classification scheme used by Park Australia.
• Oceanic shallow coral reefs: Coral reefs occurring seaward of the continental shelf break in depths shallower than 30 m.
• Oceanic mesophotic coral reefs: Coral reefs occurring seaward of the continental shelf break in in the mesophotic zone: a reduced light zone between 30 m and the maximum depth at which there is sufficient penetration of sunlight to support photosynthesis. The maximum depth is variable dependent upon water clarity and may extend to 150 m in the clearest of waters however, as a national average it is nominally defined as 70 m.
• Shallow coral reefs: Coral reefs shallower than 30 m
• Shallow rocky reefs: Rocky reefs shallow than 30 m
• Mesophotic coral reefs: Coral reefs deeper than 30 m
- NvclEcoCom (String): Natural Values Common Language classification Ecosystem Complex classification.
• Oceanic coral reefs: Coral reefs occurring seaward of the continental shelf break.
- INUNDTN (String): [Queensland Intertidal and Subtidal ecosystem Classification]: Inundation
- SMB_CMP (String): [Queensland Intertidal and Subtidal ecosystem Classification]: Structural macrobiota composition
- AS_TidalZ (String): [Seamap Australia Classification]: Aquatic Setting Tidal Zone (Intertidal or Subtidal)
- AS_BDepth (String): [Seamap Australia Classification]: Aquatic Setting Benthic Depth (Littoral, Infralittoral)
- AS_System (String): [Seamap Australia Classification]: Aquatic Setting (Marine)
- AS_SubSys (String): [Seamap Australia Classification]: Aquatic Setting (Nearshore, Offshore) Note: We have only set this with the crosswalk and so is not assigned based on the position of the feature relative to the 30 m contour that normally separates this classification. Some features are marked as 'Nearshore;Offshore' to indicate that it might be in either category.
- BC_Level1 (String): [Seamap Australia Classification]: Biotic Component (Biota Present, Biota Absent)
- BC_Level2 (String): [Seamap Australia Classification]: Biotic Component (Invertebrates, Microbes, Vegetation)
- BC_Level3 (String): [Seamap Australia Classification]: Biotic Component (Non-Molluscan Filer Feeders, Stromatolite, Macrophytes)
- BC_Level4 (String): [Seamap Australia Classification]: Biotic Component (Coral Biota, Macroalgae, Seagrass)
- SO_Level1 (String): [Seamap Australia Classification]: Substratum Origin (Anthropogenic Origin, Biogentic Origin, Geologic Origin)
- SO_Level2 (String): [Seamap Australia Classification]: Substratum Origin (Algae, Carbonate, Terrigenous)
- SO_Level3 (String): [Seamap Australia Classification]: Substratum Origin (Halimeda, Coral, Limestone)
- SC_Level1 (String): [Seamap Australia Classification]: Stratum Component (Hard Substrata, Soft Substrata)
- Area_km2 (Decimal number, length: 10, precision: 6) Area of the feature in km2. Calculated with project projection of EPSG:3112 and the QGIS field calculator expression: round($area / 1000000,6)


Location of the data:
This dataset is filed in the eAtlas enduring data repository at: data/custodian/2023-2026-NESP-MaC-3/3.17_Northern-Aus-reef-mapping/data/AU_NESP-MaC-3-17_AIMS_NW-Aus-Features

Change log:
2025-08-05 - Release of version v0-1

References:
Butler, C., Lucieer, V., Walsh, P., Flukes, E., & Johnson, C. (2017). Seamap Australia [Version 1.0] the development of a national benthic marine classification scheme for the Australian continental shelf (Final Report to the Australian National Data Service (ANDS) High Values Collection #19, p. 52). Institute for Marine and Antarctic Studies, University of Tasmania. https://seamapaustralia.org/wp-content/uploads/2018/04/Seamap_Australia_Report_18_04_18.pdf

Lawrey, E. (2024). Coral Sea Oceanic Vegetation (NESP MaC 2.3, AIMS) [Data set]. eAtlas. https://doi.org/10.26274/709g-aq12

Zann, M., Kenna, E., & Ronan, M. (2017). Queensland Intertidal and Subtidal ecosystem classification scheme Version 1.0: Module 1—Introduction and implementation of intertidal and subtidal ecosystem classification (p. 77). Department of Environment and Heritage Protection. https://wetlandinfo.des.qld.gov.au/resources/static/pdf/resources/reports/intertidal-subtidal/module-1-int-sub.pdf

Lineage

Maintenance and Update Frequency: asNeeded

Notes

Credit
This dataset collection was developed using funding from the Australian Government's National Environmental Science Program and the Australian Institute of Marine Science.