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Cape Canyon and Associated Islands, Bays and Lagoon (Cape Canyon and Surrounds)

Cape Canyon is one of two submarine canyons off the South African west coast. The EBSA includes key features surrounding the canyon as well: the adjacent shelf edge; Langebaan Lagoon; Marcus, Malgas and Jutten Islands; St Helena Bay; several small coastal MPAs; and the most persistent and intense upwelling cell on the South African west coast. The canyon and a muddy habitat on the shelf edge are habitat types of limited extent and are both Critically Endangered. The submarine canyon hosts fragile, habitat-forming species, and there are other unique and potentially vulnerable benthic communities in the area. The hard-ground areas are also likely to be susceptible to damage. This EBSA is important for pelagic fish, foraging marine mammals, and several threatened seabird species.

EBSA Description: Cape Canyon and Surrounds

General Information


Cape Canyon is one of two submarine canyons off the west coast of South Africa (the other being the Cape Point Valley) and this broader area, including St Helena Bay, has been recognized as important in three systematic conservation plans. Both benthic and pelagic features are included, and the area is important for pelagic fish, foraging marine mammals and several threatened seabird species. The canyon and a muddy habitat on the shelf edge are habitat types of limited extent and are considered Critically Endangered. There is evidence that the submarine canyon hosts fragile habitat-forming species, and there are other unique and potentially vulnerable benthic communities in the area. The hard ground areas, particularly those outside of the trawl footprint, are also likely to be susceptible to damage and there are increasing petroleum and mining applications in this area. There are several small coastal MPAs within the EBSA.

MARISMA updates

The site description has been updated, and the boundary has been revised. 

Introduction of the area

Cape Canyon and Associated Islands, Bays and Lagoon is bounded along the shore from the Sixteen Mile Beach MPA in the south to about 10 km south of Lamberts Bay in the north, extending further offshore in the southern part compared to the northern part. The focus area includes Langebaan Lagoon, Saldanha Bay, Marcus, Malgas and Jutten islands, the Cape Canyon submarine canyon and adjacent shelf edge, and has been extended to include the whole of St Helena Bay. This area was identified as a priority area through a national plan to identify areas for offshore protection (Sink et al., 2011) and by a systematic biodiversity plan for the west coast (Majiedt et al., 2013). It was also identified as an important area for pelagic ecosystems and species (Grantham et al., 2011).

Description of location

This focus area is located around the southwest coast of South Africa and is completely within South Africa’s national jurisdiction. Cape Canyon and Associated Islands, Bays and Lagoon is bounded along the shore from the Sixteen Mile Beach MPA in the south to about 10 km south of Lamberts Bay in the north, extending much further offshore (approximately 70 km) in the southern part compared to that in the northern part (<10 km).


Area details

Feature description of the area

Cape Canyon and Associated Islands, Bays and Lagoon is a productive area with important benthic and pelagic habitats and physical features that jointly support important life-history stages of species, and threatened, fragile and vulnerable species and habitats. The main geological feature of this EBSA is the Cape Canyon itself. It is one of two canyons on the South African west coast (the other being the Cape Point Valley), which has its head about 23 km offshore of Cape Colombine, at -168 m depth, and incises to a depth of about -900 m (De Wet 2012). New bathymetry data clearly show that the main channel (at the canyon head) comprises two separate, parallel channels in the northern and middle sections that combine to form a deeply incised main channel in the south that runs all the way to the outer continental slope, ending at about -3500 m in the Cape Basin (De Wet 2012). The western branch of the main channel is much more deeply incised than is the eastern branch by up to 100 m, and the slope of the western canyon margin is much steeper than that of the eastern side (De Wet 2012). Marcus, Malgas and Jutten islands are other key geological features in this EBSA, as well as the adjacent lagoon and bay system on the coast. The area includes unconsolidated sand, mud and gravel benthic habitats and a pelagic habitat type that is characterised by elevated productivity and frequent fronts associated with shelf-edge upwelling (Lutjeharms et al., 2000, Lagabrielle 2009, Roberson et al., 2017).

The key geological features, described above, in turn support important biological communities, from fragile to threatened species. These include four distinct benthic macrofaunal communities characterized by molluscs, polychaetes, amphipods and brittle stars (Karenyi 2014), and hard-ground habitats that are poorly known (Sink et al., 2012b). Fragile cold-water corals have been collected within the area. Further, a recent survey sighted seapens, anemones, starfish and cloaked hermit crabs (Sink 2016); all of which species are sensitive to impacts to the seabed. Parts of this dynamic area, particularly within St Helena Bay, experience low-oxygen water that may support unique biological communities (Sink et al., 2011) that are also sensitive to disturbances. The small islands contained in the EBSA provide breeding habitat for several endemic seabird species, most of which are threatened, or seals (Kemper et al., 2007). The area encompasses a key foraging area for marine mammals (Best 2006, Barendse et al., 2011) and two marine Important Bird Areas (Birdlife et al., 2013). The focus area has also been included in annual demersal fish trawl surveys conducted by the Department of Agriculture, Forestry and Fisheries.

Since the original description and delineation of the EBSA, new research has been conducted within the area, allowing a more comprensive understanding of the features and communities at this site. Consequently, the boundary has been revised to improve precision in representing the key benthic and pelagic habitat types and features, as well as key biodiversity features that underpin the EBSA status, such as: fragile and sensitive habitat-forming species, islands, the canyon, and key species (e.g., colonial seabirds). Much of the improvement in the delineation was based on new bathymetry data (De Wet 2012), which has allowed a more precise, data-driven boundary for the EBSA rather than an expert-based boundary. It also also based on new biological sampling that, for example, motivates for extending the EBSA to include the full extent of St Helana Bay to encompass those sensitive communities (Karenyi 2014, Sink 2016). The new boundary also better aligns with current initiatives to expand South Africa’s MPA network.

Feature conditions and future outlook of the proposed area

Habitat condition within this broad area ranges from good to poor (Sink et al., 2012a). Pressures are increasing, although the area includes several coastal MPAs (Langebaan, Sixteen Mile Beach, Marcus Island, Malgas Island and, Jutten Island) which protect habitats and species to varying extents. It has been recommended that MPAs in the area should be considered for consolidation, extension, or re-zoning to resolve existing resource conflicts, protect threatened species in their core areas, and minimize stakeholder impacts (Sink et al., 2011). The lagoon system is vulnerable to further impacts, and the islands with their associated seabird colonies are all threatened (Kemper et al., 2007). Petroleum exploration is increasing in the area, and there are new applications for seabed mining for phosphates and other minerals.


Assessment of the area against CBD EBSA criteria

 Uniqueness or rarity


Rank: Medium

Cape Canyon is one of two reported submarine canyons on the west coast of South Africa and in the southern Benguela. This area was identified by two systematic plans because of rare habitat types including the canyon, rare muds and low-oxygen benthic habitats (Sink et al., 2011, 2012a, 2012b, Majiedt et al., 2013). The Southern Benguela Muddy Shelf Edge comprises two patches off Saldahna, covering an estimated 567 km2.

 Special importance for life-history stages of species


Rank: High

The area encompasses a key foraging area for marine mammals including humpback and southern right whales (Best 2006, Barendse et al., 2011) and two marine Important Bird Areas. Closer to shore the Canyon is adjacent to several terrestrial IBAs (Bird Island, Dassen Island, Heuningnes River and estuary system, and the Lower Berg river wetlands). The seas extending from these sites have been proposed as a marine IBA for the following seabird species: African Penguin, Bank Cormorant, Cape Cormorant, Cape Gannet, Caspian Tern, Crowned Cormorant, Damara Tern, Great Crested Tern, Kelp Gull and Hartlaub’s Gull. Further offshore, along the shelf edge where commercial fisheries are concentrated, BirdLife International has identified a large area, which overlaps with the Cape Canyon area, as a potential marine IBA for Atlantic Yellow-nosed and Black-browed albatrosses and Cory’s Shearwater. Several other species (e.g. Shy Albatross and White-chinned Petrel) are likely to qualify as trigger species in this area, but tracking data or analyses are lacking. Grantham et al. (2011) also showed that this area had the highest density of breeding seabirds that feed on pelagic species. High densities of sardine and anchovy eggs contributed to the high selection frequency of this broader area in the offshore systematic biodiversity plan for South Africa (Sink et al., 2011). Spawning and nursery habitat for Cape hakes and is also included in this area (Sink et al., 2011, Kone et al., 2013).

 Importance for threatened, endangered or declining species and/or habitats


Rank: High

This area is importance for several threatened seabirds including four Endangered seabirds – African Penguin, Bank Cormorant, and Black-browed and Atlantic Yellow-nosed albatrosses. These animals are highly dependent on this area for some or all of their life stages, particularly for foraging. In addition, several species of lower conservation threat status are similarly dependent on this area: the Vulnerable White-chinned Petrel, Cape Cormorant and Cape Gannet.

The area is dominated by a wide variety of threatened ecosystem types identified in the National Biodiversity Assessment 2011 (Sink et al., 2012) and the BCC assessment Holness et al. (2014). A highly diverse set of Critically Endangered ecosystems are found in the area, namely Namaqua Boulder Shore, Namaqua Inner Shelf Reef, Namaqua Inshore Hard Grounds, Namaqua Inshore Reef, Namaqua Island, Namaqua Sandy Inshore, Namaqua Sheltered Rocky Coast, Southern Benguela Canyon, Southern Benguela Hard Shelf Edge, Southern Benguela Muddy Shelf Edge, Southwestern Cape Boulder Shore and Southwestern Cape Inshore Hard Grounds. A further four Endangered ecosystems are found in the area namely Namaqua Mixed Shore, Southern Benguela Outer Shelf Reef, Southwestern Cape Exposed Rocky Coast, Southwestern Cape Hard Inner Shelf and Southwestern Cape Island. Finally, the high diversity of threatened ecosystems includes the Vulnerable Namaqua Muddy Inshore, Namaqua Very Exposed Rocky Coast, Southern Benguela Hard Outer Shelf, Southern Benguela Sandy Shelf Edge, Southwestern Cape Lagoon, Southwestern Cape Mixed Shore and Southwestern Cape Sandy Inshore. The dominant pelagic habitat within the area is considered Vulnerable and is the most threatened of South Africa’s 16 pelagic habitat types (Sink et al., 2012a).

 Vulnerability, fragility, sensitivity, or slow recovery


Rank:  High

The submarine canyon in this area is considered vulnerable to impact because cold-water corals, gorgonians and other slow-growing, habitat-forming species were observed within this area on submersible footage (Diamondfields International unpublished footage, Sink and Samaai 2009). Gilchrist (1921) also reported cold water corals, black corals and two hundred large sponges in a single otter trawl in this area in 1920, and it was only in the 1990s that trawling was initiated in the hard-ground habitats within this area (Sink et al., 2012b). Deep reefs and hard grounds in the area are also likely to host fragile three-dimensional, habitat-forming species, although this has not been confirmed by in-situ research. These habitats are all considered sensitive to demersal trawling and mining (Sink et al., 2011, 2012a, 2012bb). The low-oxygen habitats and likely biological communities they support are also considered vulnerable.

 Biological productivity


Rank: High

The most persistent and intense upwelling cell on the entire South African west coast is found within this area at Cape Columbine, resulting in the area downstream having the highest productivity, organic loading (Demarq et al., 2007) and organic carbon deposits on the seafloor (Bailey 1991) on this coast. St Helena Bay has also been identified as the area having the most persistent oxygen-deficient water in the region (Bailey 1991). South of Cape Columbine, a different set of oceanographic features dominate, and frequent pulse upwelling events result in high productivity over shorter periods (Demarq et al., 2007). Cape Canyon and Surrounds includes part of the area with highest copepod biomass on the west coast (Grantham et al., 2011). Large populations of marine top predators forage and/or breed within the area, including several species of seabirds, cetaceans and seals (Best 2006, Barendse et al., 2011, Hutchings et al., 2012).


 Biological diversity


Rank: Medium

South Africa’s national habitat map indicates many ecosystems in this area (Sink et al., 2012 a), and this diversity of habitat types is a key driver of this area’s selection in two systematic biodiversity plans (Sink et al., 2011, Majiedt et al., 2013). The submarine canyon, sand and mud habitats, patches of low oxygen water, islands and the adjacent lagoon system contribute to the high habitat diversity in this area (Sink et al., 2011,2012a, Majiedt et al., 2013).




Rank: Medium

There is a moderate level of naturalness within this area. Of the two mapped submarine canyons, there is lower trawling effort and fewer pressures in the Cape Canyon, which is the closer canyon to the city of Cape Town (Sink et al., 2011, Sink et al., 2012a,b). Some of the canyon habitat is outside of the trawling footprint, and there are adjacent hard ground areas that are also untrawled (Wilkinson 2009, Sink et al., 2012b). However, there is a port at Saldanha, and several fisheries sectors operate within this area.



Bailey, G. W. 1991. Organic carbon flux and development of oxygen deficiency on the modern Benguela continental shelf of 22°S: spatial and temporal variability. Pages 171-183 in R. V. Tysen and T. H. Pearson, editors. Modern and Ancient Continental Shelf Anoxia. Geological Society.

Barendse J, Best PB, Thornton M, Elwen SH, Rosenbaum HC, Carvalho I, Pomilla C, Collins TJQ, Meÿer MA, Leeney RH. 2011. Transit station or destination? Attendance patterns, regional movement, and population estimate of humpback whales Megaptera novaeangliae off western South Africa based on photographic and genotypic matching. In: Kirkman S, Elwen SH, Pistorius PA, Thornton M, Weir C (eds), Conservation biology of marine mammals in the southern African subregion. African Journal of Marine Science 33: 353–373.

Best PB. 2006. The presence of right whales in summer on the west coast of South Africa: the evidence from historical records. African Journal of Marine Science 28: 159–166.

BirdLife International. 2013. Marine e-Atlas: Delivering site networks for seabird conservation. Proposed IBA site ‘Atlantic, Southeast 19 – Marine’. Available online: Accessed 11 March 2013

Demarcq, H., R. Barlow, and L. Hutchings. 2007. Application of a chlorophyll index derived from satellite data to investigate the variability of phytoplankton in the Benguela ecosystem. African Journal of Marine Science 29:271-282.

Gilchrist JDF. 1921. Report of the Fisheries and Marine Biological Survey for the year 1920 1: 1-27.

Grantham HS, Game ET, Lombard AT, Hobday AJ, Richardson AJ, Beckley LE, Pressey RL, Huggert JA, Coetzee JC, van der Lingen CD, Petersen SL, Merkle D, Possingham HP. 2011. Accomodating dynamic oceanographic processes and pelagic biodiversity in marine conservation planning. PLoS ONE 6: e16552. DOI:10.1371/journal.pone.0016552.

Hutchings L, Jarre A, Lamont T, van den Berg M, Kirkman SP. 2012. St Helena Bay (southern Benguela) then and now: muted climate signals, large human impact. African Journal of Marine Science 34: 559–583

Kemper J, Underhill LG, Crawford RJM, Kirkman SP. 2007. Revision of the conservation status of seabirds and seals breeding in the Benguela Ecosystem. In: Kirkman SP (ed.) Final Report of the BCLME (Benguela Current Large Marine Ecosystem) Project on Top Predators as Biological Indicators of Ecosystem Change in the BCLME. Avian Demography Unit, Cape Town, pp 325–342.

Koné, V. Lett, C., Fréon, P. 2013. Modelling the effect of food availability on recruitment success of Cape anchovy ichthyoplankton in the southern Benguela upwelling system, African Journal of Marine Science, 35:2, 151-161.

Lagabrielle E. 2009. Preliminary report: National Pelagic Bioregionalisation of South Africa. Cape Town: South African National Biodiversity Institute.

Majiedt P, Holness S, Sink K, Oosthuizen A, Chadwick P. 2013. Systematic Marine Biodiversity Plan for the West Coast of South Africa. South African National Biodiversity Institute, Cape Town.

Sink K and Samaai T. Identifying Offshore Vulnerable Marine Ecosystems in South Africa, Unpublished Report for South African National Biodiversity Institute, pp. 29

Sink KJ, Attwood CG, Lombard AT, Grantham H, Leslie R, Samaai T, Kerwath S, Majiedt P, Fairweather T, Hutchings L, van der Lingen C, Atkinson LJ, Wilkinson S, Holness S, Wolf T. 2011. Spatial planning to identify areas for offshore biodiversity protection in South Africa. Unpublished Report. Cape Town: South African National Biodiversity Institute.

Sink K, Holness S, Harris L, Majiedt P, Atkinson L, Robinson T, Kirkman S, Hutchings L, Leslie R, Lamberth S, Kerwath S, von der Heyden S, Lombard A, Attwood C, Branch G, Fairweather T, Taljaard S, Weerts S, Cowley P, Awad A, Halpern B, Grantham H, Wolf T. 2012a. National Biodiversity Assessment 2011: Technical Report. Volume 4: Marine and Coastal Component. South African National Biodiversity Institute, Pretoria.

Sink KJ, Wilkinson S, Atkinson LJ, Sims PF, Leslie RW, Attwood CG. 2012b. The potential impacts of South Africa’s demersal hake trawl fishery on benthic habitats: historical perspectives, spatial analyses, current review and potential management actions. Unpublished report. Cape Town: South African National Biodiversity Institute.

Wilkinson S. 2009. Ring Fencing the Trawl Grounds. South African Deep-sea Trawling Industry Association. Report prepared by Capricorn Fisheries Monitoring cc. Cape Town.

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EBSA criteria met at a high (red), medium (orange) or low (yellow) rank. 


Download the revised EBSA description:

icon Cape Canyon and Associated Islands, Bays and Lagoon 2018 (1.85 MB)


Download the revised EBSA boundary:

icon Cape Canyon and Associated Islands, Bays and Lagoon KMZ 2018 (279.53 kB)


Download a map of the revised EBSA:

icon Cape Canyon and Associated Islands, Bays and Lagoon 2018 (1.83 MB)