Most of South Africa's coastline is exposed to waves with relatively few sheltered areas. Bays are special because they provide shelter from waves and storms, and because they retain water and concentrate plankton (including the tiny larvae of most marine creatures including fish). They provide us with harbours, seafood, safe swimming opportunities and beautiful beaches.

St Helena Bay on the productive west coast is an important nursery ground for commercially exploited fish, and is known for its frequent low oxygen events. Cape Bays, such as Saldahna and Table Bay, have a long history in supporting trade, fisheries, aquaculture and tourism. False and Walker Bay were famous for their fishing opportunities and at night the sounds of whales breathing can sometimes be heard during whale season. Reefs in False Bay host different species to those on the Atlantic coast and are popular destinations for scuba divers. They have also supported more than 100 years of linefishing, both commercial and recreational. On the south coast, bays such as Algoa Bay near Port Elizabeth feature many endemic species found only in South Africa.

Bays are ecosystems under pressure, since port, harbour and coastal developments, fish farms and waste water discharge are often concentrated in these special places. Bays also retain pollutants and can experience increased impacts of Harmful Algal Blooms (sometimes known as red or black tides) leading to fish kills, rock lobster walkouts and human health impacts. The cause of increased Harmful Algal Blooms are not well understood, but agricultural fertilizer runoff, depletion of filter feeding fish, invasive species and climate change are likely contributing factors.

Monitoring the ecology of bays, as well as good catchment management, effective fisheries management and the prevention of invasive alien species are important measures to keep bays healthy. Effective management of bays relies on regulating coastal developments, ports and harbours, shipping and fisheries, maintaining water quality and generating opportunities for tourism. Marine Spatial Planning is a key tool that can help balance social, economic and environmental interests in these busy socio-ecological systems.

Important bay ecosystems that will receive increased protection include Algoa Bay in the Addo Elephant National Park MPA.

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