A variety of anthropogenic factors, including overexploitation of stocks, pollution, and poaching, combined with low compliance and poor enforcement of fisheries management strategies, like bag limits and minimum sizes, were not effective at preventing the decline of several economically important species.

It can facilitate visitor access and allow traditional local community benefit to continue without excessive ecological damage by over-utilisation of sensitive areas.

[6] The Table Mountain National Park Marine Protected Area includes the seabed, the water, and the airspace above it to an altitude of 1000 metres above sea level.

[10] Other major risks to the MPA are assessed as over-utilisation of resources and pollution by city storm water outlets, sewage effluent dispersal systems and rivers,[9] There is a lack of integration of the physical, biological and social aspects into a coherent management plan, which has been attributed to a lack of capacity and infrastructure, and excessive bureaucratic process on the part of the government.

[5] Periodical assessment of MPA management in South Africa has found that limited human resources in skilled staff, non-compliance and lack of monitoring and community education are unresolved problems.

Tourist attractions inside the MPA include scuba diving, boat-based whale and shark-watching, snorkelling with seals and high-speed scenic boat rides.

This MPA has some of the most intensively studied waters on South Africa due to the presence of universities, the natural history museum and several marine research institutes in and near Cape Town, so more is known about the local biodiversity than most other MPAs in South African waters[2] Further use opportunities have been identified in education, monitoring and research, tourism and recreation development, and contributions to local economy through poverty alleviation and partnerships.

[5] Fishing is allowed in the controlled zone of the MPA subject to permits,[12] regulations, catch limits and seasons set by the Department of Agriculture, Forestry and Fisheries.

Some of them are listed here for the west coast of the peninsula from north to south, and for the east coast, also from north to south, roughly following the coastline: Atlantic seaboard:[15] False Bay west:[15] Events and functions, including races, professional film and stills shoots require a permit for the specific occasion and must be booked ahead of time through SANParks.

The main exception is a long ridge of sedimentary rock that extends in a southward direction from off the Strand, to approximately level with the mouth of the Steenbras River.

Most of these are granite of the Peninsula pluton, but east of Seal Island they are generally sandstone, either of the Table Mountain series, or the underlying Tygerberg formation.

A large granite reef, Whittle Rock, lies on the eastern edge of the MPA about halfway between the north shore and the mouth of the bay.

An interesting local phenomenon is the contact zone between the intrusive granite of the Peninsula pluton and the older Malmesbury strata visible at the Sea Point shoreline.

Just outside the bay, there is a large shoal area at Rocky Bank, a relatively shallow area around Cape Pont, with two large pinnacles at Bellows Rock and Anvil Rock, and a long ridge extending south-west from Cape Hangklip, which channels cold, nutrient-rich water into the west side of the bay during upwelling events.

Even today, in spite of technical advances and improved weather forecasting this still happens, though less frequently than in the past, and recently the salvage operations are more often successful.

The more southerly position of this high pressure zone in summer has the effect of blocking the cold fronts, and restricting them to pass mostly south of the continent.

[27][28] Most of the energy of swells with a significant westerly component does not make it round the corner of Cape Point into the west side of False Bay.

The Cape Point break is considered to be a relatively distinct change in the bioregions and this can be clearly seen from the difference in the ecologies between the Atlantic seaboard of the peninsula and False Bay, though there is a significant overlap of resident organisms.

The coastline in this region was considerably lower during the most recent ice-ages, and the detail topography of the dive sites was largely formed during the period of exposure above sea level.

This means that sessile organisms must be specifically adapted to areas of relatively loose substrate to thrive in them, and the variety of species found on a sandy or gravel bottom will depend on all these factors.

Sandy bottoms have one important compensation for their instability, animals can burrow into the sand and move up and down within its layers, which can provide feeding opportunities and protection from predation.

[5] The more prominent red seaweeds of the west coast of the Cape Peninsula include several species of foliose algae, including Botryocarpa prolifera, Botryoglossum platycarpum, Epymenia capensis, Epymenia obtusa, Gigartina bracteata, Neuroglossum binderianum, Pachymenia carnosa, Plocamium corallorhiza, Thamnophyllis discigera, and Thammnophyllis pocockiae.

South African abalone stocks are severely threatened as a result of long term over-exploitation and uncontrolled large-scale poaching, and ecological changes in parts of its distributional range.

These can be mitigated to some extent by expanding the protected area so that some of the change can be absorbed more gradually and there is greater redundancy of habitats, allowing more options for localised migration.

[5] Oils spills, Plastic, Heavy metals, Sewage, Invasive species are one of the biggest threats to a natural ecosystem, as they can cause complex and far reaching changes to the structure and dynamics of the communities, with a risk of severely affecting biodiversity.

[5] Simon’s Town and Hout Bay harbours have many alien species, which is attributed to a high frequency of local and international vessel movement.

At least two marine species that have become truly invasive affect this MPA - Carcinus maenas, the European shore crab, and Mytilus galloprovincialis, the Mediterranean mussel.

[5] The proximity to several universities and research institutions in Cape Town has led to many studies of the ecology of the MPA and the organisms found in it, particularly those that are easily collected.

As of 2023, the survey continues in False Bay, mostly by Wreckless Marine, which is doing the deeper waters, and Council for Geoscience which is working the shallower areas to the northeast with a smaller vessel.

The survey found that the divers lacked knowledge of the regulations, guidelines, and codes of conduct, and those who looked for the information could not find it, as it was not made available to the public even where it existed.