Habitat Mapping

Page review/updated 25/09/2023

The equipment used most frequently by D&S IFCA, for habitat mapping and ground truthing work, is the Flying Array camera system which was designed by Dr Emma Sheehan at Plymouth University. 

It is a camera system mounted on a sledge, which maintains itself just above the seabed in order to prevent damage to the benthic substrate.

To maintain the correct buoyancy while towing, four pressure resistant plastic tubes are mounted on the top of either side of the sledge making it slightly positively buoyant. A short chain maintains contact with the seabed and as the chain makes more or less contact with the seabed the sledge adjusts its height.

A High Definition Bowtech camera, with a live feed umbilical, is attached to the sledge at a 45º angle along with three lights and two lasers.  The lasers are set 50cm apart and are used for the scaling of the footage. The Flying Array is deployed from a gantry on the stern of D&S IFCA’s research vessel Black Jack.

Drift transects are carried out for approximately 20 minutes at an ideal speed of 0.5 knots to cover a distance of approximately 200m. This will vary depending on the conditions of each location surveyed. 

D&S IFCA uses a range of other cameras and sonars to carry out habitat mapping and ground-truthing.


Seagrass is one of the features of the Torbay Marine Conservation Zone and the conservation objective for the seagrass beds is to “recover to favourable condition”.

In January 2014, D&S IFCA implemented, through the permit conditions of the Mobile Fishing Permit Byelaw, no access areas in the Torbay part of Lyme Bay and Torbay SC for demersal mobile gear vessels, to protect the sensitive reef habitats. These measures also protected the seagrass feature of the Torbay MCZ.

In order to ensure that the management in place is appropriate to protect the seagrass, all known seagrass beds within Torbay are surveyed using towed camera systems biennially to determine the density and extent of the beds. The surveys began in 2012 before the beds were protected from towed demersal gear. The camera used is a Bowtech dive camera with a light which is lowered over the side of the research vessel in a housing that can be towed. Drift transects are carried out across the beds, based on previous years maps, ensuring to cover as much as the bed as possible and getting the full picture of the outer extent. The density levels of the seagrass and co-ordinates are recorded in real time whilst watching the live footage from a monitor on board the vessel. The footage is recorded so that it can be reviewed at a later date if necessary. The results are mapped in the office and compared to previous surveys. The 2017 survey saw the area of seagrass beds increase since 2014, by a total of 10%. The largest increase in area (8 ha) was 29% for the Broadsands to Elberry seagrass bed, the two sperate beds recorded in 2014 had merged.

Reports with full results are available for 20122014 and 2017.

The 2019 survey was carried out by the Environment Agency in collaboration with Natural England as part of the development of a Water Framework Directive (WFD) tool to assess the ecological status of subtidal seagrass in estuarine and coastal waterbodies. D&S IFCA supplied maps of the seagrass beds for the planning stage and assisted during the survey. The survey was carried out on the Research Vessel Three Rivers, which is a 6.2m Cheetah catamaran, using a traditional drop-down cameras survey method and a novel echosounder survey. A GoPro camera was mounted onto a 1m² drop-down quadrate and at pre-determined points a still image of the seabed was taken, and presence or absence of seagrass was recorded. These data can be used to estimate extent and percentage cover and provides ground-truthing for the echosounder work. The echosounder survey took place using a BioSonics DT-X Extreme Echosounder attached to the side of the vessel. Transects were carried out to cover the full extent of the larger beds. The echosounder survey can be used to measure seagrass extent, maximum depth and density. The results of the survey will be complied by the EA and shared with D&S IFCA when complete. D&S IFCA will then use these results to ensure the management currently in place is still appropriate.

There are also seagrass beds in a number of other locations in the D&S IFCA’s District including in Plymouth Sound and the Yealm, and Salcombe Estuary. The surveys for these locations are now carried out by NE and the EA with the data being shared with D&S IFCA. The IFCA carried out a survey in Salcombe in 2014, the report for this can be found here.


In 2016 underwater filming was carried out in Lyme Bay using the Flying Array camera system in an area which is protected from towed demersal gear. This was to survey the habitats in areas that fall outside the Special Area of Conservation but are protected by the Statutory Instrument (SI). This was to have a better understanding of the area if the SI was ever removed. A total of 40, 20 minute underwater video tows were recorded over three locations in the SI, covering a range of depth from 4 to 30 metres. EUNIS biotope classification was undertaken by Ocean Ecology Ltd. A total of seven broad-scale habitats were identified across the Lyme Bay SI with the majority of stations characterised by ‘A5.4 Subtidal mixed sediment’.

In addition to the habitat analysis a scallop count was undertaken to get an understanding of the stock in the closed area. Three scallop taxa were identified in two of the locations; the king scallop (Pectin maximus), queen scallop (Aequipectin sp.) and scallops there were unidentifiable to species/genus level and were therefore recorded as Pectinidae. Counts of scallops were recorded as count per unit hour, with the averages being 480 plus/minus 65 (mean plus/minus  SE) and 466 plus/minus  76.

The full report can be found here.


In January 2014, D&S IFCA closed the majority of the Start Point to Plymouth Sound and Eddystone SAC (within its District) to towed demersal gear to protect the reef feature of the site under the Mobile Fishing Permit Byelaw. The closure included an area at the northern End of Zone 2 (known as the ‘triangle’) of the South Devon Inshore Potting Agreement, which was traditionally open to towed demersal gear from 1st January to 31st May inclusive. Much of this area does not include the reef feature however, due to the narrow access to the site between the reef and no means of monitoring the site other than during patrols, D&S IFCA decided to close the whole area with the understanding that this closure would be reviewed if the correct monitoring systems were put in place such as inshore vessel monitoring systems (iVMS).

Due to the possibility of reviewing the access area, and due to uncertainties put forward by the fishing industry suggesting that some of the areas was sand banks rather than rock, D&S IFCA undertook additional survey work on the Prongs and surrounding areas of the SPPSE SAC to verify the existing feature map which was mapped using acoustic data.

The work was undertaken using the Flying Array camera system towed from D&S IFCA’s research vessel Black Jack. This video footage was then analysed by Ocean Ecology Ltd. The results indicated that much of the area was made up of circalittoral coarse sediment rather than rock. The full report can be found here:   

The full report covers a larger scope than the ‘Prongs’ area. Underwater camera surveys were carried out across the Start Point to West Rutts section of the SPPSE SAC during 2013 and 2014 as part of a PhD with Plymouth University assessing the impact of potting on benthic habitats. As the camera work had been carried out it was seen as a good opportunity to ground truth the location and extent of the Designated features in this area. As an addition to this analysis, a pink sea fan (Eunicella verrucosa) condition assessment was undertaken in order to provide Natural England information on the distribution and condition of this fragile species to inform their ongoing condition assessment of the site.


In June and August 2015 further underwater camera work was carried out in the Start Point to Plymouth Sound and Eddystone (SSPSE) SAC and neighbouring Plymouth Sound and Estuaries SAC, to cover areas which were not surveyed in the previous years. The areas surveyed were the reefs in Bigbury Bay and an area known as the Pinnacles to the South close to the six mile limit. The purpose of this filming work was to ground truth the location and extent of the designated features. The Flying Array was deployed from RV Black Jack, and 25 video tows were undertaken at the Pinnacles site and 11 tows in the Bigbury Bay area. The two survey sites were very different in their characterisation, with Bigbury Bay being largely made up of extensive high energy bedrock reef dominated by macrophytes including kelp, red and brown algae. The Pinnacle reef areas were generally characterised by expanses of low rock covered with a sediment veneer and large outcrops surrounded by areas of muddy sand and gravel. There were high densities of pink sea fans forming expansive meadows with Alcyonium digitatum among dense hydroid/bryozoan turf. The full analysis and report can be found here.


D&S IFCA joined Natural England and the Environment Agency to carry out filming work using a drop-down camera system and grab sampling in the Lundy SAC. This survey was carried out on an EA vessel with an IFCA officer on board to assist.

The objectives of the work were: to collect data to investigate the structure, function and distribution of biological communities in the SAC; to collect habitat characterisation data to provide information on a possible future impact study in the area which is targeted by demersal trawl gear for a squid fishing; to assess the impact of management on the diversity and composition of benthic communities in space and time; and to collect incidental records of spiny lobsters across the site.

The analysis and report writing is in progress and once the results are available the report will be published on our website.