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NOAA and Analytic Laboratories of Hawai‘i (ALH): Benthic Habitat Mapping Program Partnership

Background and Overview:

In response to the growing concern over the global degradation of coral reefs, President Clinton issued the Coral Reef Protection Executive Order 13089 in June 1998. This order established the U. S. Coral Reef Task Force (CRTF), which includes the major federal agencies responsible for for aspects of coral reef conservation along with state and territorial partners. The final National Action Plan to Conserve Coral Reefs was developed by the CRTF based on the collective experience of a large number of coral reef specialists both inside and outside of the government. One of the major action items in this document calls for the mapping of all U. S. Coral Reefs. In order to meet the objective the CRTF established the Mapping and Information Synthesis Working Group. Over the course of nearly two years this working group of the CRTF developed the Mapping Implementation Plan (MIP).

The initial aerial survey and habitat mapping work in support of the Mapping Implementation Plan in the Pacific was initiated by NOAA‘s Center for Coastal Monitoring and Assessment (CCMA) Biogeography Program. The initial phase of this project ("Benthic Habitats of the Eight Main Hawaiian Islands") is intended to develop methodology and serve as the model for mapping the other U. S. Pacific islands. During the summer of 2000 NOAA‘s National Ocean Service (NOS) and National Geodetic Survey (NGS) acquired aerial color photography and for approximately one third of the near shore waters of the eight Main Hawaiian Islands. In addition, hyperspectral imagery was obtained simultaneously for several test sites (e.g. Kāne‘ohe Bay, West Hawai‘i, South Moloka‘i) and IKONOS satellite imagery will be obtained for comparative evaluations.

CRAMP has been involved in development of the CRTF Mapping Implementation Plan from the beginning. The need to integrate monitoring and assessment activities with the mapping and habitat classification work drew CRAMP into a co-operative relationship with NOAA. Analytical Laboratories of Hawai‘i (ALH), an eleven year old Hawai‘i based company, was awarded the NOAA contract to provide aerial photo and hyperspectral image interpretation and GIS map production for the pilot study. Thus a collaborative effort between NOAA, ALH and CRAMP was formed. NOAA, under the leadership of Mark Monaco is responsible for the overall mapping and classification at the national level including Hawai‘i. ALH under S. Miles Anderson is responsible locally for all aspects of the NOAA Hawai‘i mapping program and for preparation of the benthic habitat maps for Hawai‘i. CRAMP under Paul Jokiel is providing NOAA and ALH with field support and the biological expertise needed for the mapping and ground truth effort in Hawai‘i. In addition, CRAMP has been in a co-operative agreement with USGS for the Hawai‘i reef mapping and assessment program for the past two years. USGS is one of the federal partners in the CRTF effort. The USGS Hawai‘i program has a number of objectives, one of which involves the interpretation of remote sensing data and mapping of Hawaiian coral reefs. CRAMP participation in the NOAA and USGS investigations will benefit all of the partners in the CRTF mapping effort.

Benthic mapping survey of Kāne‘ohe Bay, September 2000. Team members (left to right facing camera) include Mark Monaco (NOAA Project Director), Mike Coyne (NOAA, habitat classification), Russ Ives (NOAA, hyperspectral analysis), Will Smith (CRAMP field support) and Miles Anderson (ALH classification and mapping). Boat being piloted by Ross Langston of HIMB. Photo by Paul Jokiel.

Preparation of GIS Maps Depicting Benthic Habitats of the Hawaiian Islands

S. Miles Anderson

Analytic Laboratories of Hawai‘i

1320 Aalapapa

Lanikai, Hawai‘i 96734

(808) 262-2417

Project Description:

A primary product of this effort will be an ArcView format benthic habitat map and geographic information system (GIS) produced by interpreting the remote sensing data. ALH will produce this output by manual delineation of habitats from the aerial photographs and application of analysis software applied to the hyperspectral digital imagery. Benthic features are being classified using a hierarchical classification scheme. The scheme was developed in the Caribbean by NOAA‘s Center for Coastal Monitoring and Assessment Biogeography team and modified to meet the habitat structure for Hawai‘i through a series of meetings, workshops and reviews by marine resource managers of the West Pacific. Upon completion of the mapping effort, a comparative analysis will be conducted to determine accuracy of the maps prepared from each of the remote sensing methods. As the mapping and remote sensing products are completed, they will be posted on the Internet at

Four potential study areas have been selected for this work. The two priority sites are Kāne‘ohe Bay on O‘ahu and a section of the North Kona coast on the west side of the Island of Hawai‘i. Two additional sites have been selected, one on the South Shore of Moloka‘i and a second in West Maui.

Eight project milestones have been identified:

  1. Critique, field test and update coral reef habitat classification scheme

  2. Refine the custom, NOS-designed ArcView software extension for coral reef mapping activities

  3. Photo interpret color imagery and generate GIS maps of benthic habitats in ArcView format for each study area

  4. Photo interpretat hyperspectral imagery and generate GIS maps of benthic habitats in ArcView format for each study area

  5. Ground truth each mapped area generating attributed GPS data according to specified standards and provide an accuracy assessment identifying the percent of correctly identified polygons for each study area

  6. Generate NGDC format metadata for all digital geographic data produced during this tenure

  7. Prepare comparative analysis of accuracy of benthic habitat maps based on color vs. hyperspectral aerial photo interpretation

  8. Finalize the classification scheme, proceed with data fusion, complete final report and proceed with photo interpretation and GIS map preparation for the eight Main Hawaiian Islands

Project Status (November 2000)

The habitat classification scheme has been critiqued and is in the process of being updated. The NOAA habitat digitizing extension for ArcView has been customized and coral reef benthic habitat field validation points have been collected in Kāne‘ohe Bay and on the Kona Coast. These data are being used for ground truthing of color aerial photography and hyperspectral image interpretation. The surveys also serve as an initial test of the Hawai‘i Benthic Habitat Classification Scheme for Mapping the Main 8 Hawaiian Islands.

Field Validation Methods

Approximately fifty points within the major habitat categories are collected for each study site. The data are generated as evenly as possible across sub-categories and zones. The major habitat types are:

  • Unconsolidated Sediments

  • Sand

  • Mud

  • Submerged Aquatic Vegetation

  • Macroalgae

  • Seagrass

  • Coral Reef and Hard Bottom

  • Coral Reef and Colonized Hard Bottom

  • Uncolonized Hard Bottom

  • Encrusting/Coralline Algae

The major habitat types are subdivided into 27 separate benthic coral reef habitat types.

Randomly located habitat validation field assessment sites were generated using a random point generator obtained from the Environmental Systems Research Inc. (ESRI) web site. This software generates an ArcView shape file composed of random points inside an ArcView GIS polygon shape. Polygons of the study areas have been digitized from geo-referenced NOAA navigational charts projected in UTM Zone 4 on NAD 83 datum. The extent of the study area polygon for Kāne‘ohe Bay included the Sampan channel on the south end, northward to Chinaman‘s Hat and from shore to a depth of approximately 40 feet outside the barrier reef. Random points were generated within the polygon and point and area benthic habitat assessments were conducted at each location. The extent of the study area polygon for Kona is defined by the north end of Kawaihae Harbor to the south edge of Kiholo Bay and from shore to the 10 fathom contour and the field survey were conducted on November 5-12, 2000.

Waypoint files were generated from the random point files and all points that could be safely accessed were navigated to using a Trimble GeoExplorer 3 GPS data logger. Upon arriving at the waypoint, the boat was anchored, allowed to stabilize down wind. A weighted meter line was dropped and the point of contact with the bottom was classified by the biologists. At that time, GPS logging began to establish the exact position of the data point. Twenty GPS positions were collected at 5-second intervals for each survey site. The points were averaged to obtain a single position.

Miles Anderson uses GPS to log position of lead line while Will Smith prepares to dive to bottom of Kaneohe Bay in order to classify the habitat type. Photo by Paul Jokiel.

Miles Anderson uses GPS to log position of lead line while Will Smith prepares to dive to bottom of Kāne‘ohe Bay in order to classify the habitat type. Photo by Paul Jokiel.

The point assessment was conducted by surveying the benthic habitat within 0.5 meter of the point where the weight landed. The area data was generated in the same way except the area surveyed included a distance of approximately a 7-meter radius from the weight. The depth of the site was recorded and the benthic habitat assessment was made using a glass bottom look box, diving or observing from the surface. Benthic habitat point data was recorded on the GPS data logger using a custom data dictionary designed to meet the specifications of the Coral Reef Habitat Classification Scheme. Area data was entered in waterproof notebooks and transferred to the GIS by hand. Underwater photographs were taken to create a visual record of habitat types as well as document areas where the coral reef habitat classification scheme proved uncertain.

Data were collected to determine spatial accuracy. A convenient point from the random point file was navigated to on five of the field days and a GPS fix was recorded. Also on field days, a fixed monument on land was visited and GPS data recorded.

When an area that was particularly interesting, benthic habitat assessments were conducted that were not included in the random point set. These were assigned letters A through J to distinguish them from the random point assessments, which were assigned numerical site identifiers.

A GIS was prepared in ArcView GIS format and the data are also summarized in an Excel spreadsheet.

Summary of Preliminary Results

1. Kāne‘ohe Bay Survey

Chart of Kaneohe Bay showing points classified to date.

Chart of Kāne‘ohe Bay showing points classified to date. (Click for a larger view)

During the period of the Kāne‘ohe Bay field survey, sea and wind conditions prevented safe boating and diving access to the reef crest and forereef. Thus, habitat types such as encrusting coralline algae and pavement with sand channels, which are characteristic of the barrier reef crest and forereef, were not frequently encountered. These areas will be surveyed as weather conditions permit. The location of the Kāne‘ohe Bay habitat assessments conducted to date is illustrated. A total of 300 random benthic habitat point and area assessments have been made in Kāne‘ohe Bay during this survey. The data generated by the Biogeography Team during the field work of April 5 to April 11, 2000 and the areas of interest have been appended to the data set as an Excel spreadsheet and as separate shape files in the GIS. With the appended data included, 352 sites have been assessed in Kāne‘ohe Bay. A summary of the Kāne‘ohe Bay benthic habitat assessments per major and detailed habitat group is presented.

2. Kona, Hawai‘i Survey

Distribution of data points collected at Kona.

Distribution of data points collected at Kona. (Click for a larger view)

The Kona Survey Team consisted of (left to right): Paul Jokiel, Will Smith, Miles Anderson and Capt. Mark Chesler of Neptune Charlies. Photo by DeeAnn Chesler.

The Kona Survey Team consisted of (left to right): Paul Jokiel, Will Smith, Miles Anderson and Capt. Mark Chesler of Neptune Charlies. Photo by DeeAnn Chesler.

Approximately 300 randomly located habitat validation field assessment sites for Kona were visited and evaluated in the same manner during November 5-12, 2000. The same procedures used in the Kāne‘ohe Bay field survey were followed. The vessel navigated to pre chosen random points. The Captain held on station while a weighted line was thrown overboard and a float clipped to hold the line nearly vertical. Miles Anderson took precise position using the GPS. The biologists (Jokiel and Smith) then entered the water and classified the habitat at the point of contact made by the lead weight using skin diving or SCUBA methods. In shallow water the classification could be done from the surface using a look box. In extremely shallow water the survey was made using a kayak launched from the survey vessel. In areas of surf or extremely shallow water the work was accomplished by swimming or wading into the site using a water proof box for the GPS unit. A summary of data points collected at Kona is presented.

Shallow water survey method. Miles Anderson (forward) establishes position with GPS while Will Smith uses look box to classify benthic type. Photo by Paul Jokiel.

Shallow water survey method. Miles Anderson (forward) establishes position with GPS while Will Smith uses look box to classify benthic type. Photo by Paul Jokiel.



Last Update: 04/21/2008

By: Lea Hollingsworth


Hawai‘i Coral Reef Assessment & Monitoring Program

Hawai‘i Institute of Marine Biology

P.O. Box 1346

Kāne‘ohe, HI 96744

808-236-7440 phone

808-236-7443 fax