Aquatic biomes include both freshwater and marine biomes. The marine biome is divided into three main ecosystems: the oceans, coral reefs and estuaries. South Africa has a coastline that is over 3000 kilometres in length and it features coral reefs on its eastern coastline and numerous estuaries along its length.

Ocean ecosystems are divided into four zones that, broadly speaking, are differentiated by their proximity to the shoreline and by their depth. The intertidal zone is along the shoreline. Further out is the pelagic zone, and beneath that is the benthic zone, which includes the sea floor. The deepest and darkest zone is referred to as the abyssal zone.

As the tide goes out the rock pools are gradually exposed along the intertidal edge of Sodwana Bay, KwaZulu-Natal. High vegetated dunes can be seen on the other side of the bay

In South Africa the intertidal shoreline may be sandy or rocky. For many of us, our commonest experiences of the ocean are along the shoreline. For a previous post on the fascination of rock pools in the intertidal zone see here.

This sandy inlet between rocky outcrops seems to invite one into its sheltered waters decorated with tumbled pebbles, crushed shells and floating kelp. I took this photo on a visit to Onrus in the Overberg region of the Western Cape

Life abounds in the intertidal zone and includes also a variety of seabirds adapted to the marine environment, some of which nest on rocky shores or on dunes or sandy beaches above the high tide line.  Nesting birds are very vulnerable to human activity on the beaches. I discuss more of this issue in a previous post on the suburban seaside.

African black oystercatchers foraging in the intertidal zone near Hermanus in the Western Cape. Their diet includes limpets, mussels and crustaceans. Oystercatchers are ground nesters and their nests, little more than a scrape on the ground, are very vulnerable to disturbances

Flocks of terns and seagulls on the rocky shoreline at Onrus, Western Cape

A closer look at the terns and gulls congregating on the shoreline

The terns are particularly exquisite in flight. There is an abundance of kelp growing in the tidal waters of this small bay at Onrus

The eastern coastline and the eastern side of the southern coastline of South Africa adjoins the Indian Ocean, and west of that and up the western side of South Africa the coastline adjoins the colder waters of the Atlantic Ocean. Cape Agulhas, a headland on the south coast in the Overberg region of the Western Cape marks the point at which the two oceans officially meet.

Cape Agulhas, where two oceans meet

The plaque marking the officially designated point along the coastline where the Indian and Atlantic oceans meet at Cape Agulhas

Many living organisms and animals are harvested from the sea to feed and sustain the human population. Sadly, overharvesting has become a threat to many populations of fish and other creatures. Other significant threats to the marine biome are climate change, which is associated with a significant increase in water temperature and pollution.              

Colourful small-scale fishery boats looking picturesque at the Hout Bay harbour near Cape Town in 2004

For those who eat fish, the South African Sustainable Seafood Initiative (SASSI) helps direct retailers, consumers and people who fish to use the more sustainable species using a colour-coded system where species on the green list are more sustainable, species on the orange list less so, and those on the red list are unsustainable and/or illegal to sell in South Africa. See the full SASSI list here:

Also available from SASSI are easy tools to aid making more sustainable choices while shopping or eating out, including an app that can be downloaded to one’s phone and a pocket guide – see

I photographed these long-lines and hooks in a fishing boat in Hout Bay harbour in 2004. Long-line fishing is notorious for its indiscriminate by-catch, which frequently includes non-target species of fish and even turtles, seabirds and other creatures

In addition to over-harvesting, pollution has a severe effect on the marine biome and on individual species. A local example of the effect of pollution on fish species is reported in a peer-reviewed study done on fish caught by small-scale commercial fishermen at Kalk Bay near Cape Town. Fifteen different chemical compounds were tested for in the fish fillets, gills, liver and intestines of fish tested. The fish tested were from random daily commercial catches sold at Kalk Bay harbour in late 2017 and included snoek, hottentot (Cape bream) and panga according to an article in Groundup reporting on the study.

Compounds that were present in various body parts of the fish included pharmaceuticals such as analgesic/anti-inflammatories, an antibiotic and an anti-epilectic drug and a disinfectant and various industrial chemicals found in pesticides, flame retardants and personal care products. All compounds represent a level of risk when consumed by humans. The presence of pharmaceuticals arises because Cape Town pumps about 37 million litres of untreated sewage out to sea per day.

In addition, partially treated waste-water also finds its way into the sea as well as direct run-off from stormwater drains that is discharged into streams or rivers or directly into the sea. For more details about this report see here:

Freshwater from the lagoon flowing into Sodwana Bay just after dawn as the coastal fog is rising

For some relief from such hectic information, the above photo was taken at Sodwana Bay, in the iSimangaliso Marine Protected Area which is part of the iSimangaliso Wetland Park. This conservation area is on the UNESCO World Heritage list and it includes protection of  coastal and offshore marine life, notably providing nesting sites along its shores for loggerhead and leatherback turtles.

The Sodwana area is world famous for its offshore coral reefs, which attract scuba divers to venture out to explore what really is a wonderland in the clear waters just off the coast.

The skipper looks for a gap in the breakers before taking scuba divers out to the coral reefs off shore from Sodwana Bay. My spouse is one of the divers on board. For a short account of my brief foray into scuba diving see here

Unless one uses lights underwater, the deeper one dives the more of the colour spectrum fades away as the light gets filtered through the water. Despite this limitation here are a few photos that my spouse managed to take while diving on the reefs.

This part of the coral reef must be fairly shallow as red is still visible. Red is the first part of the colour spectrum to be filtered out, and disappears at a depth of about 4.5 m (15 feet), orange being the next to go. Yellow is still visible at a depth of 10.6 to 12 m (35–40 ft)

Corals seen in filtered light – many of these corals are likely greyish in colour even in unfiltered light

A marine turtle foraging on the reef. Judging from the slightly hooked beak this is a loggerhead turtle, the most common turtle in South African waters. It nests in protected areas along the northeastern coast of KwaZulu-Natal

Bright yellow turret corals growing in small clusters

A shoal of yellow snappers. These fish occur on coral reefs to a depth of about 40 m (130 feet)

Meanwhile, back on the shore the lagoon, which was closed off from the sea by a barrier at the time, reflects the sky. The relationship of the freshwater lagoon to the sea is constantly changing – sometimes the sand barrier is so narrow that the high tide washes into the lagoon, and sometimes the barrier is breached and the lagoon flows directly into the sea

I almost got bogged down in discussions as to the difference between lagoons and estuaries, but the terms are often used rather vaguely and also can be used interchangeably. It seems safe to say that lagoons can be regarded as a subset of estuaries. Estuaries form where rivers flow into the ocean and they are often partially or even completely enclosed from the sea but there are times where there is an inflow and outflow of freshwater and water from the sea at high tide. Estuaries are one of the three major ecosystems identified in the marine biome.

Part of the Kosi Bay estuary system with it traditional system of fish traps in place with the Indian Ocean beyond. The Kosi Bay system comprises a complex of four lakes connected by channels and wetlands leading into the relatively narrow channel at its mouth into the ocean

A view from the shoreline of one of the Kozi Bay lakes with the line of high dunes between the lake system and the ocean visible against the skyline. Several years ago we went on a 4-day hike around the Kozi Bay estuary system, but the photographs we took were on film. Perhaps one of these days I should digitise the prints and do a blog post on this interesting hike

Estuaries are very dynamic systems with salinity levels varying as freshwater and seawater levels are constantly changing with the tide and seasonally or in the longer term due to environmental factors such as rainfall and human activities that divert groundwater away from the system. For example, thirsty tree plantations can have a major impact on freshwater supplies to an estuary as happened at the Lake St Lucia estuary, which forms part of the iSimangaliso Wetland Park. Controversies over the management of the Lake St Lucia estuary remain ongoing. Active human interventions over the decades include diverting the Mfolozi river away from the lake to the benefit of sugar farming, and more recently restoring the old path of the river into the lake. A further source of debate and controversy is when and how the sand barrier at the mouth into the sea should be breached. Most recently the mouth was breached using earth removing equipment in January 2021. For more see here.

A view of a section of the Lake St Lucia estuary during a prolonged period of drought. Mostly mud and very little standing water is visible in the darker area surrounded by dry sand. In what used to be more usual times the sandy areas would be underwater. This photograph was taken in January 2016

The above photo was taken in February 2019 not far from the previous photo, but after the end of the severe drought with much more water in Lake St Lucia

Resident organisms in estuarine systems have to be able to cope with fluctuations in salinity levels, but estuaries also attract many visiting species. Estuaries can act as breeding grounds or nurseries for visiting marine species and they provide food and shelter for migrating species of birds. Many different habitat types exist in and around estuaries. Estuaries also play an important role as filters of both sediments and pollutants that may be present in river systems. Estuaries also act as buffer systems along shorelines.

This large body of freshwater in the Overberg region of the Western Cape is situated alongside the seashore (separated by dunes). It is known variously as the Klein River Estuary or Lagoon  – illustrating the interchangeability of the terms estuary and  lagoon. A section of the estuary is a declared bird sanctuary. Just as for Lake St Lucia, there are ongoing controversies as to when and where the barrier between the estuary and the sea should be artificially breached (or even if at all)

Greater flamingos foraging in the water flowing out from the Klein River estuary into the ocean

Globally estuaries and wetlands are all too often drained to make way for urban settlement. It can only be hoped that the estuaries that still remain are appropriately protected.

A view of part of the Langebaan Lagoon Marine Protected Area, an important estuarine system on the western coast of South Africa

Included in the habitats supported by the estuarine system and in the offshore protected area in the Langebaan Lagoon Marine Protected Area are rocky reefs that support kelp forests – for more detail see here.

The reason I specifically mention the kelp forests is because I want to link to the documentary My Octopus Teacher that was filmed in the kelp forest offshore from Simonstown near Cape Town. The film has won numerous awards, including the BAFTA for best documentary and most recently an Oscar, also for best documentary.

The documentary is based on the most astounding footage of an octopus in the kelp forest who develops an undeniable bond with Craig Foster, a naturalist and free diver (he did not use scuba gear, snorkling gear or a wetsuit), who literally and figuratively immersed himself in the icy waters surrounding the kelp forest.

For more about the making of the film directed by Pippa Ehrlich and James Reed, and produced by Craig Foster, and the decisions made about how to frame the story, see

Also on the website is more information about the kelp forests The Sea Change Trust was founded by Craig Foster and Ross Frylinck in 2012 and in the ensuing Sea Change Project the project team engages in story telling for ocean protection. On the website the ‘About page’ explains:  

“We are a team of media and science professionals dedicated to connecting people to the wild through incredible stories backed by scientific knowledge. Our goal is to contribute to the long-term protection of South Africa’s marine environment by making the Great African Seaforest a global icon. Our work includes films, books, exhibitions, marine biology research through living science, and impact campaigns”.


Carnie Tony. 2021. Oom Rudi and the bulldozers: SA’s largest estuarine lake mouth smashed open. Daily Maverick 168. 9 January.

IUCN. [n.d.] Ocean Warming. IUCN Issues Brief.

Kretzmann, Steve. 2019. Pharmaceuticals and industrial chemicals found in fish caught off Cape Town’s coast. City’s waste is ending up in its fish. Groundup. 25 June.

Lindsey, Rebecca. 2021. Climate Change: Global Sea Level. National Oceanic and Atmospheric Administration. January 25.

UNESCO. [n.d.] iSimangaliso Wetland Park.

WikiMili. 2021. Langebaan Lagoon Marine Protected Area.

Posted by Carol