Underwater photo-transect surveys were conducted on September 23-27, 2007 at different sections of the reef flat, reef crest and reef slope in Heron Reef. This survey was done by swimming along pre-defined transect sites and taking a picture of the bottom substrate parallel to the bottom at constant vertical distance (30cm) every two to three metres. A total of 3,586 benthic photos were taken. A floating GPS setup connected to the swimmer/diver by a line enabled recording of coordinates of transect surveys. Approximation of the coordinates for each benthic photo was based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software. Coordinates of each photo were interpolated by finding the the gps coordinates that were logged at a set time before and after the photo was captured. The output of this process was an ArcMap point shapefile, a Google Earth KML file and a thumbnail of each benthic photo taken. The data in the ArcMap shapefile and in the Google Earth KML file consisted of the approximated coordinate of each benthic photo taken during the survey. Using the GPS Photo Link extension within the ArcMap environment, opening the ArcMap shapefile will enable thumbnail to be displayed on the associated benthic cover photo whenever hovering with the mouse over a point on the transect. By downloading the GPSPhotoLink software from the www.geospatialexperts.com, and installing it as a trial version the ArcMap exstension will be installed in the ArcMap environment.

The output of this process was an ArcMap point shapefile, a Google Earth KML file and a thumbnail of each benthic photo taken. The data in the ArcMap shapefile and in the Google Earth KML file consisted of the approximated coordinate of each benthic photo taken during the survey. Using the GPS Photo Link extension within the ArcMap environment, opening the ArcMap shapefile will enable thumbnail to be displayed on the associated benthic cover photo whenever hovering with the mouse over a point on the transect.

By downloading the GPSPhotoLink software from the www.geospatialexperts.com, and installing it as a trial version the ArcMap extension will be installed in the ArcMap environment.

Underwater georeferenced photo-transect survey was conducted on September 23 - 27, 2007 at different sections of the reef flat, reef crest and reef slope in Heron Reef. For this survey a snorkeler or diver swam over the bottom while taking photos of the benthos at a set height using a standard digital camera and towing a surface float GPS which was logging its track every five seconds. A standard digital compact camera was placed in an underwater housing and fitted with a 16 mm lens which provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by three fin kicks of the survey diver/snorkeler, which corresponded to a surface distance of approximately 2.0 - 4.0 m. The GPS was placed in a dry-bag and logged its position as it floated at the surface while being towed by the photographer. A total of 3,586 benthic photos were taken. A floating GPS setup connected to the swimmer/diver by a line enabled recording of coordinates of each benthic. Approximation of coordinates of each benthic photo was done based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the gps coordinates that were logged at a set time before and after the photo was captured. Benthic or substrate cover data was derived from each photo by randomly placing 24 points over each image using the Coral Point Count excel program (Kohler and Gill, 2006). Each point was then assigned to 1 out of 80 cover types, which represented the benthic feature beneath it. Benthic cover composition summary of each photo scores was generated automatically using CPCE program. The resulting benthic cover data of each photo was linked to gps coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 56 South.

Underwater georeferenced photo-transect surveys were conducted on October 3-7, 2012 at various sections of the reef and lagoon at Lizard Island, Great Barrier Reef. For this survey a snorkeler swam while taking photos of the benthos at a set distance from the benthos using a standard digital camera and towing a GPS in a surface float which logged the track every five seconds. A Canon G12 digital camera was placed in a Canon underwater housing and photos were taken at 1 m height above the benthos. Horizontal distance between photos was estimated by three fin kicks of the survey snorkeler, which corresponded to a surface distance of approximately 2.0 - 4.0 m. The GPS was placed in a dry bag and logged the position at the surface while being towed by the photographer (Roelfsema, 2009). A total of 1,265 benthic photos were taken. Approximation of coordinates of each benthic photo was conducted based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the GPS coordinates that were logged at a set time before and after the photo was captured. Benthic or substrate cover data was derived from each photo by randomly placing 24 points over each image using the Coral Point Count for Microsoft Excel program (Kohler and Gill, 2006). Each point was then assigned to 1 of 79 cover types, which represented the benthic feature beneath it. Benthic cover composition summary of each photo scores was generated automatically using CPCE program. The resulting benthic cover data of each photo was linked to GPS coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 55 South.

Underwater georeferenced photo-transect surveys were conducted on December 10-15, 2011 at various sections of the reef at Lizard Island, Great Barrier Reef. For this survey a snorkeler or diver swam over the bottom while taking photos of the benthos at a set height using a standard digital camera and towing a GPS in a surface float which logged the track every five seconds. A standard digital compact camera was placed in an underwater housing and fitted with a 16 mm lens which provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by three fin kicks of the survey diver/snorkeler, which corresponded to a surface distance of approximately 2.0 - 4.0 m. The GPS was placed in a dry-bag and logged the position as it floated at the surface while being towed by the photographer. A total of 5,735 benthic photos were taken. A floating GPS setup connected to the swimmer/diver by a line enabled recording of coordinates of each benthic photo (Roelfsema 2009). Approximation of coordinates of each benthic photo was conducted based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the GPS coordinates that were logged at a set time before and after the photo was captured. Benthic or substrate cover data was derived from each photo by randomly placing 24 points over each image using the Coral Point Count for Microsoft Excel program (Kohler and Gill, 2006). Each point was then assigned to 1 of 78 cover types, which represented the benthic feature beneath it. Benthic cover composition summary of each photo scores was generated automatically using CPCE program. The resulting benthic cover data of each photo was linked to GPS coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 55 South.

Underwater georeferenced photo-transect surveys were conducted at different locations: in the shallow waters of the Reef Flat (0.5-2.5m) by a snorkeller, or, along a 5m depth contour of the Reef Slope by a diver. For these surveys, the snorkellers or divers traversed a pre-determined transect 250-1000 m in length, while taking photos of the benthos at a set height using a standard digital camera and towing a surface float GPS which was logging its track every five seconds. The camera lens provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photoquadrats was estimated by fin kicks of the surveyor, and corresponded to a surface distance of approximately 2.0 - 4.0 m. The coordinates of each photoquadrat were approximated based on the timestamp of the photoquadrat and the GPS timestamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photoquadrat were interpolated by finding the GPS coordinates that were logged at a set time before and after the photoquadrat was captured. Photoquadrats were collected with the purpose of determination of the benthic composition of each photoquadrat and to subsequently use this georeferenced field data for calibration and validation of benthic habitat maps. Transect location, direction and depth were chosen for this purpose and so as to characterise the variation in benthic cover types present on coral reefs. Photoquadrat interval along the transects was chosen to reflect the resolution of high spatial resolution satellite image data types. As the data is being made available publically prior to publication, for any downloads, please provide the following information to the authours: - Personal details and institution - Provide a brief paragraph as to the intended use of the data. - Cite the data appropriately.

Underwater georeferenced photo-transect survey was conducted on September 16-21, 2009 at different sections of the reef flat, reef crest and reef slope in Kubulau, Fiji. For this survey a snorkeler or diver swam over the bottom while taking photos of the benthos at a set height using a standard digital camera and towing a surface float GPS which was logging its track every five seconds. A standard digital compact camera was placed in an underwater housing and fitted with a 16 mm lens which provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by three fin kicks of the survey diver/snorkeler, which corresponded to a surface distance of approximately 2.0 - 4.0 m. The GPS was placed in a dry-bag and logged its position as it floated at the surface while being towed by the photographer. A total of 9,646 benthic photos were taken. A floating GPS setup connected to the swimmer/diver by a line enabled recording of coordinates of each benthic (Roelfsema and Phinn, 2009).Approximation of coordinates of each benthic photo was done based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (http://www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the gps coordinates that were logged at a set time before and after the photo was captured. Dominant benthic or substrate cover type was assigned to each photo by placing 1 points over each image using the Coral Point Count excel program (Kohler and Gill, 2006). Each point was then assigned a dominant cover type, which represented the dominant benthic/substrate feature in the whole photo. Using a hierarchical benthic cover scheme containing four first-level categories (Coral, Algae, Seagrass, Non-living) and thirty second-level categories that was derived from Knudby et al. 2011. Benthic cover composition summary of each photo scores was generated automatically using CPCE program. The resulting benthic cover data of each photo was linked to gps coordinates, saved as an ArcMap point shapefile, in Geographic Coordinate System WGS 1984.

For these surveys, a snorkeler(s) swam over the bottom while taking photos of the benthos at a set height using a standard digital camera and towing a surface float GPS which was logging its track every five seconds. The camera lens provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by fin kicks of the survey snorkeler, and corresponded to a surface distance of approximately 2.0 - 4.0 m. Approximation of coordinates of each benthic photo was done based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the gps coordinates that were logged at a set time before and after the photo was captured. Dominant benthic or substrate cover type was assigned to each photo by placing 24 points random over each image using the Coral Point Count excel program (Kohler and Gill, 2006). Each point was then assigned a dominant cover type. Using a benthic cover type classification scheme containing seven first-level categories (seagrass, seagrass plus, macro algae calcareous, macro algae non calcareous, cyanobacteria and other algae, substratum, and, other) and 41 subcategories. Benthic cover composition summaries of each photo were generated automatically in CPCe. The resulting benthic cover data for each photo was linked to gps coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 56 South.

georeferenced dive and snorkel photo-transect surveys were conducted at different locations surrounding Lizard Island, Australia. For the surveys, a snorkeler or diver swam over the bottom at a depth of 1-2m in the lagoon, One Tree Beach and Research Station areas, and 7m depth in Watson's Bay, while taking photos of the benthos at a set height using a standard digital camera and towing a surface float GPS which was logging its track every five seconds. The camera lens provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by fin kicks, and corresponded to a surface distance of approximately 2.0 - 4.0 m. Approximation of coordinates of each benthic photo was done based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the gps coordinates that were logged at a set time before and after the photo was captured. Dominant benthic or substrate cover type was assigned to each photo by placing 24 points random over each image using the Coral Point Count excel program (Kohler and Gill, 2006). Each point was then assigned a dominant cover type using a benthic cover type classification scheme containing nine first-level categories - seagrass high (>=70%), seagrass moderate (40-70%), seagrass low (<= 30%), coral, reef matrix, algae, rubble, rock and sand. Benthic cover composition summaries of each photo were generated automatically in CPCe. The resulting benthic cover data for each photo was linked to GPS coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 56 South. The OBIA class assignment followed a hierarchical assignment based on membership rules with levels for "reef", "geomorphic zone" and "benthic community" (above).

Underwater georeferenced photo-transect surveys were conducted at different locations and using slightly different methodologies. Photoquadrats were collected with the purpose of determination of the benthic composition of each photoquadrat for subsequent use as georeferenced field data for calibration and validation purposes of benthic habitat maps derived from remote sensing satellite or airborne imagery. Transect location, direction and depth were chosen to characterise the variation of benthic cover types represented on coral reefs. Photoquadrat interval along the transects was chosen to reflect the resolution of the satellite image data types used.In principle a diver or snorkeler captures a photoquadrat (approximate 1 m2 footprint) of the bottom along a transect at 2 - 3 m intervals. Images were assigned a GPS coordinate and analysed for benthic composition.Initially, from 2002 to 2006, divers/snorkelers swam along a 50 m transect tape. Coordinates were recorded at the beginning and end of the tape. Knowing the horizontal distance interval between photoquadrats the coordinates could be approximated for each image.From 2007 to 2017, divers/snorkelers towed a floating GPS at the surface which was logging position. The coordinates of each photoquadrat were synchronised based on the timestamp of the photoquadrat and the GPS timestamp, using specialised software (e.g. GPS Photo Link www.geospatialexperts.com or DNR Garmin). In principle coordinates of each photoquadrat were interpolated by finding the GPS coordinates that were logged at a set time before and after the photoquadrat was captured. The camera lens provided a 1 m x 1 m footprint, at a 0.5 m height above the benthos using a plumb line. Horizontal distance between photoquadrats was estimated by fin kicks of the surveyor, and corresponded to a surface distance of approximately 2 - 4 m.For these surveys, the snorkelers traversed a pre-determined transect 250-1000 m in length, varying depending on heterogeneity of the area covered. Divers would conduct 30 min dives along a 5m depth contour, which would be approximately 500-700 m in length.

An object based image analysis approach (OBIA) was used to create a habitat map of the Lizard Reef. Briefly, georeferenced dive and snorkel photo-transect surveys were conducted at different locations surrounding Lizard Island, Australia. For the surveys, a snorkeler or diver swam over the bottom at a depth of 1-2m in the lagoon, One Tree Beach and Research Station areas, and 7m depth in Watson's Bay, while taking photos of the benthos at a set height using a standard digital camera and towing a surface float GPS which was logging its track every five seconds. The camera lens provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by fin kicks, and corresponded to a surface distance of approximately 2.0 - 4.0 m. Approximation of coordinates of each benthic photo was done based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the gps coordinates that were logged at a set time before and after the photo was captured. Dominant benthic or substrate cover type was assigned to each photo by placing 24 points random over each image using the Coral Point Count excel program (Kohler and Gill, 2006). Each point was then assigned a dominant cover type using a benthic cover type classification scheme containing nine first-level categories - seagrass high (>=70%), seagrass moderate (40-70%), seagrass low (<= 30%), coral, reef matrix, algae, rubble, rock and sand. Benthic cover composition summaries of each photo were generated automatically in CPCe. The resulting benthic cover data for each photo was linked to GPS coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 56 South. The OBIA class assignment followed a hierarchical assignment based on membership rules with levels for "reef", "geomorphic zone" and "benthic community" (above).

Underwater georeferenced photo-transect survey was conducted on May 5-9, 2013 at different sections of the reef flat, reef crest and reef slope in Roviana Reef, Solomon Islands. For this survey a snorkeler or diver swam over the bottom while taking photos of the benthos at a set height using a standard digital camera and towing a surface float GPS which was logging its track every five seconds. A standard digital compact camera was placed in an underwater housing and fitted with a 16 mm lens which provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by three fin kicks of the survey diver/snorkeler, which corresponded to a surface distance of approximately 2.0 - 4.0 m. The GPS was placed in a dry-bag and logged its position as it floated at the surface while being towed by the photographer. A total of 9378 benthic photos were taken. A floating GPS setup connected to the swimmer/diver by a line enabled recording of coordinates of each benthic. (Roelfsema and Phinn, 2009).Approximation of coordinates of each benthic photo was done based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (http://www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the gps coordinates that were logged at a set time before and after the photo was captured.Dominant benthic or substrate cover type was assigned to each photo by placing 24 points random over each image using the Coral Point Count excel program (Kohler and Gill, 2006). Each point was then assigned a dominant cover type. Using a benthic cover type classification scheme containing ten first-level categories (Coral, Algae, Seagrass, Non-living) and 64 subcategories that were derived from Roelfsema et al. 2013.Benthic cover composition summary of each photo scores was generated automatically using CPCE program. The resulting benthic cover data of each photo was linked to gps coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 57 South.

This paper describes seagrass species and percentage cover point-based field data sets derived from georeferenced photo transects. Annually or biannually over a ten year period (2004-2015) data sets were collected using 30-50 transects, 500-800 m in length distributed across a 142 km**2 shallow, clear water seagrass habitat, the Eastern Banks, Moreton Bay, Australia. Each of the eight data sets include seagrass property information derived from approximately 3000 georeferenced, downward looking photographs captured at 2-4 m intervals along the transects. Photographs were manually interpreted to estimate seagrass species composition and percentage cover (Coral Point Count excel; CPCe). Understanding seagrass biology, ecology and dynamics for scientific and management purposes requires point-based data on species composition and cover. This data set, and the methods used to derive it are a globally unique example for seagrass ecological applications. It provides the basis for multiple further studies at this site, regional to global comparative studies, and, for the design of similar monitoring programs elsewhere. Underwater georeferenced photo-transect surveys were conducted at different locations in the shallow waters (0.5-2.5m) of the Eastern Banks seagrass meadows, Moreton Bay, Australia. For these surveys, a snorkeler(s) swam over the bottom while taking photos of the benthos at a set height using a standard digital camera and towing a surface float GPS which was logging its track every five seconds. The camera lens provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by fin kicks of the survey snorkeler, and corresponded to a surface distance of approximately 2.0 - 4.0 m. Approximation of coordinates of each benthic photo was done based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the gps coordinates that were logged at a set time before and after the photo was captured. Dominant benthic or substrate cover type was assigned to each photo by placing 24 points random over each image using the Coral Point Count excel program (Kohler and Gill, 2006). Each point was then assigned a dominant cover type. Using a benthic cover type classification scheme containing seven first-level categories (seagrass, seagrass plus, macro algae calcareous, macro algae non calcareous, cyanobacteria and other algae, substratum, and, other) and 41 subcategories. Benthic cover composition summaries of each photo were generated automatically in CPCe. The resulting benthic cover data for each photo was linked to gps coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 56 South. Acknowledgments Funding provided by: University of Queensland; CSIRO; Cooperative Research Centre Coastal Zone, Estuaries and Waterways Management; ARC Linkage Grant to Prof. J Marshall and Prof. S Phinn; and UQ-UWA Collaborative Research Grant Prof. van Niel. Fieldwork support was provided by: Seagrass Watch Volunteers, Staff and students at the University of Queensland and the UQ Moreton Bay Research Station. WorldView-2 Imagery provided by Digital Globe and ongoing support of Trimble for use of Ecognition.NoteThe 2015 data was additional data that was collected in the same manner as the other years. Although it was not used in the publication, we believed that it should be added to the data set as it expands the collection for anyone wanting to use the data in their own way.