Muddy ecosystem types are different from sandy, rocky and other seabed habitats because of the high silt and clay content of muddy sediments. Visual tools such as camera surveys are seldom useful to sample muddy ecosystems as visibility is usually poor in mud habitats. Muds are rich and fertile, and home to many burrowing animals, some of which penetrate more than a metre into the seabed. The burrowing activities of animals in muddy habitats help exchange nutrients and cycle oxygen and minerals between the sediment and the water column. Key seafood species that rely on muddy habitats in South Africa include important species such as soles; kobs such as kabeljou or daga salmon; silver kob and snapper kob; spotted grunter; prawns, langoustines and crabs.

In South Africa, mud habitats are quite rare, occupying a far smaller area than most other ecosystem types on the shelf. Deep water muds are more widespread but likely to be more sensitive, as deep, calm mud habitats encounter little natural disturbance. Shallow mud habitats are more variable as they rely on river input, therefore reduced fresh water flow can threaten the very existence of the muds. Other pressures on muddy ecosystems include trawling, drilling for petroleum and seabed mining. Reference areas are needed so that South African scientists can study the role of marine muds and understand the impacts of trawling and petroleum activities. This will inform wise management of these ecosystems and their valuable resources.

Important mud ecosystems are included in uThukela Banks MPANamaqua Fossil Forest MPAAgulhas Mud MPA and Benguela Mud MPA.