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Prioritizing Seagrass Restoration Sites
Study examines predictors of seagrass bed recovery
By Amy V. Uhrin and Kevin Kirsch


Ecologic researchers are modeling the impact of vessel grounding to seagrass beds using GIS in the Florida Keys National Marine Sanctuary. The surface creation tools in the ArcGIS 3D Analyst extension help assess both the damage and recovery of these seagrass beds.

Modeling vessel groundings in GIS is helping determine the extent of the damage suffered by seagrass beds and identify factors that contribute to their recovery.

photo of a vessel grounding site
A vessel grounding site with propeller scar, berm, and blowhole features.

Seagrass beds are an integral component of the Florida Keys National Marine Sanctuary (FKNMS) ecosystem with nearly 1.4 million acres of seagrass growing within sanctuary boundaries. Seagrass beds provide nurseries, feeding grounds, settlement sites, and refuge areas for a large number of commercially and ecologically important shellfish and finfish species. The ability of seagrass beds to reduce current velocities, dampen wave energy, and stabilize sediments enables this coastal resource to afford shoreline protection and habitat stability during storm events.

Propeller Scars, Blowholes, and Berms

Each year, more than 600 motorized vessel groundings are reported in the FKNMS, primarily within seagrass beds. Vessel groundings result in the formation of at least one of three injury features: propeller scars, blowholes, and berms.

Propeller scars occur as a boat's propeller tears into seagrass blades and the underlying sediment creating a shallow, narrow, linear trench that is typically devoid of plants. As the boat continues to move forward, the hull of the boat digs into the seagrass bed and may eventually come to rest. It is not uncommon for the boat operator to attempt to "power off" the seagrass bed by fully engaging the engine, resulting in a deep, large excavation called a blowhole.

Much of the sediment that is excavated from the blowhole is blown onto the seagrass bed fringing the blowhole creating a berm. Because vessel groundings directly remove seagrass plants, these events have the ability to alter the abundance and distribution of many marine organisms as well as the local hydrology, resulting in an unstable seagrass bed and environmental modification on a local scale.

click to enlarge
Injury feature outlines, the bathymetric grid layer generated from sensor records, and blowhole area and volume calculations using the surface analysis tools in the ArcGIS 3D Analyst extension

Given the continued popularity of marine recreation activities, such as scuba diving and fishing, as well as commercial fishing in the Florida Keys, vessel groundings will continue to occur. Within FKNMS, natural resources such as seagrasses are protected. Any party responsible for the loss, injury, or destruction of a sanctuary resource is liable to the United States for assessment and restoration of the damaged resources.

Assessing Damage

As government trustees, the National Oceanic and Atmospheric Administration (NOAA) and the Florida Department of Environmental Protection are authorized to seek restitution from the responsible parties. Since 2000, the two agencies have cooperatively conducted impact assessments and drafted restoration plans for vessel injuries to seagrass resources utilizing protocols and analyses established under the auspices of the Mini-312 Seagrass Restoration Program ( [The program is named for a section of the National Marine Sanctuaries Act.]

Mapping for Managing Restoration

This assessment protocol incorporates several facets of GIS to determine the extent of damage to a site and monitor its recovery. Grounding sites are mapped by physically tracing the outline of the features (i.e., berm, blowhole) that result from the vessel grounding using a differential GPS. In this case, Trimble GPS Pathfinder Pro XR receiver and Trimble TSC1 data collector were used. For shallow sites, the differential GPS (DGPS) antenna is pole mounted and outlines are traced by walking the injury perimeter. Where deeper water precludes walking, the DGPS unit is attached to an inflatable boat that is then floated around the injury perimeter under the direction of a snorkeler. Injury feature coordinates are downloaded to Trimble GPS Pathfinder Office software, then exported into ArcGIS. Using ArcMap, the extent of the damaged area is calculated in square meters.

To restore a blowhole to the natural grade of the undisturbed seafloor surrounding requires determining the amount of sediment that has been excavated. To estimate this volume, NOAA researchers integrated a Lowrance LCX-15MT, a commercially available depth sounder, with the DGPS unit and mounted the system on the stern of a small inflatable boat. A bathymetric survey of the injury site is recorded as georeferenced depth soundings logged while the boat is slowly floated back and forth across the blowhole. Care is taken to collect a sufficiently dense scattering of points to describe the topographic variations (i.e., the peaks and valleys) within the blowhole.

click to enlarge
Three-dimensional representation of the volume of a blowhole that resulted from a vessel grounding. The blowhole perimeter is indicated with a black line, and the berm is indicated with a brown line.

The resulting files are downloaded to Trimble GPS Pathfinder Office software and exported to ArcGIS. An interpolated bathymetric grid surface that was limited to the area of the blowhole was created using the inverse distance weighting (IDW) function, a tool available from ArcToolbox when the ArcGIS Spatial Analyst or 3D Analyst extensions are loaded. The small interpolation areas (ranging from 10 to 500 square meters) combined with concentrated depth records made IDW an ideal technique for interpolating the bathymetric surface of blowholes. Blowhole volume was calculated in cubic meters using the Surface Analysis tool available with the ArcGIS 3D Analyst extension.

Three-dimensional images of blowholes are generated by first applying ordinary kriging to the sensor records file by choosing Interpolate to Raster from the ArcGIS 3D Analyst toolbar. The kriging layer was opened in ArcScene, an application in the 3D Analyst extension, and the layer properties were manipulated to generate the desired three-dimensional effect.

Benefits of GIS Use

The accuracy of GIS technology and its use in the Mini-312 Seagrass Restoration Program has enabled NOAA to georeference the occurrence of vessel groundings in the FKNMS as well as to gather critical data on the size, shape, and volume of damage that is used in drafting restoration plans and preparing settlement claims. The ability to accurately return to a grounding site to conduct follow-up assessments allows NOAA to compare the natural recovery of the site over time. Modeled recovery projections are a means of evaluating the overall success of the program and determining which restorative actions (if any) are required on a per-incident basis.

The authors selected 27 documented vessel grounding cases that occurred in the FKNMS for reassessment. They examined the extent of natural recovery in the absence of mitigated restoration. Indications that a damaged site is recovering include decreases in the original area and volume of a blowhole and significant seagrass regrowth in the area.

By teasing apart the relationships between the level of observed natural recovery and specific characteristics of the damage (such as when it occurred and the original volume of the blowhole), in addition to environmental parameters (such as sediment type and wave exposure), the authors expect they will be able to provide sanctuary managers with a model that can be used for predicting the potential recovery dynamics of a given site based on threshold values for the previously listed parameters. This will allow managers to set restoration priorities for recent grounding events.

Initial modeling results indicate that, although all of the parameters have been found to contribute to natural recovery (or lack thereof), the date of the grounding and a site's level of exposure to wave energy are the prominent factors. Groundings that have occurred within the last two years and were highly exposed to wave energy experienced minimal recovery. The ability to set restoration priorities will greatly enhance the Mini-312 Seagrass Restoration Program's efficiency by targeting restoration to damaged sites most at risk of expanding with the passage of time.

The authors continue to refine the model with the inclusion of additional case reassessment data as it becomes available from sanctuary staff. For more information on the Mini-312 Seagrass Restoration Program, visit NOAA's Damage Assessment, Remediation, and Restoration Program at For more information on this article, contact Amy V. Uhrin at


Kirsch, K. D., K. A. Barry, M. S. Fonseca, P. E. Whitfield, S. R. Meehan, W. J. Kenworthy, and B. E. Julius. 2005. "The Mini-312 Program—An Expedited Damage Assessment and Restoration Process for Seagrasses in the Florida Keys National Marine Sanctuary," Journal of Coastal Research. SI40: pp. 109–119.

For More Information

To find out more about three-dimensional modeling in GIS, see Learning ArcGIS 3D Analyst, a Web course available at

About the Authors

Amy Uhrin
Amy V. Uhrin

Amy V. Uhrin is a research ecologist at NOAA's Center for Coastal Fisheries and Habitat Research in Beaufort, North Carolina. She began her career with NOAA in 2000, and her research interests include disturbance ecology and recovery dynamics of seagrass ecosystems, seagrass restoration ecology, and fishing gear impacts on marine ecosystems. She holds a master's degree in biological oceanography from the University of Puerto Rico, Mayagüez.

Kevin Kirsch
Kevin Kirsch

Kevin Kirsch is a regional resource coordinator with NOAA's Office of Response and Restoration in St. Petersburg, Florida, where he responds to hazardous materials and vessel groundings and assesses the impact of these events on the marine environment. He began his career with NOAA in 2000 and spent five years assessing impacts to seagrass resulting from vessel groundings in the FKNMS. He holds a master's degree in marine science from the University of South Alabama.

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