Freshwater fish, sharks, rays, endemic plants and iconic mammals are among the country’s fastest-declining species, as invasive species, reduced freshwater flows and pollution intensify. (Wikimedia Commons)
South Africa’s wildlife and natural ecosystems are facing an accelerating decline, with the country’s most comprehensive biodiversity stocktake warning of deepening ecological stress across almost every landscape and ocean region.
The National Biodiversity Assessment 2025, released earlier this week, paints a stark picture of collapsing freshwater systems, intensifying illegal wildlife trade, surging extinction risks and the destabilisation of natural systems under climate change.
Produced by the South African National Biodiversity Institute with input from nearly 500 experts from 110 institutions, the fourth iteration of the assessment synthesises thousands of datasets across terrestrial, freshwater, coastal and marine ecosystems, as well as genetic diversity and species assessments, offering a national environmental health check.
The analysis warns that South Africa is losing ecological resilience at a rate that threatens long-term water security, food systems and economic stability.
The country is one of 17 megadiverse countries, with exceptional species richness, high levels of endemism and three of the world’s 36 biodiversity hotspots. Nature underpins the economy, jobs, food and water security and climate resilience, making it central to national development priorities.
But this ecological infrastructure is in trouble. According to the analysis, nearly half of the 986 ecosystem types assessed are threatened, with estuaries, wetlands, rivers and coasts most at risk. More than three-quarters are represented in protected areas, leaving 24% unprotected. Rivers, wetlands and estuaries have the lowest coverage.
Of 20 248 plant species, 16% are threatened, and out of 5 226 animal species, 10% are threatened, with freshwater and cartilaginous fishes (sharks, rays and chimaeras) most at risk. Overall, 70% of plant species and 77% of mammal, reptile, bird, amphibian, and freshwater fish species are well protected.
Biodiversity underpins both the country’s economy and its society, said Bernice Swarts, the deputy minister of forestry, fisheries and environment, at the report’s launch.
“Biodiversity is not just an environmental concern — it is an economic asset. It supports over 400 000 jobs, particularly in rural areas, through conservation, restoration, ecotourism and sustainable harvesting,” she said.
“When we invest in biodiversity, we invest in people, in livelihoods, in the future of our youth and in the resilience of families and communities.”
The report equips authorities with evidence-based insights to guide policy, strengthen governance and mobilise collective action across government, business and civil society, she added.
Heavy climate impacts
More than 200 species, such as the iconic halfmens — a rare, spiny desert tree — and the Namaqua dune mole-rat, have experienced severe population declines due to climate change.
Ocean prey shifts are reducing seabird numbers, coral reefs are experiencing “the worst bleaching ever recorded”, while estuarine fish ranges are extending hundreds of kilometres, altering food webs.
Climate change, too, amplifies pressures from invasions, habitat loss, pollution, and altered freshwater flows.
South Africa is expected to become drier in the west and wetter in the east, with interior regions warming faster than the global mean, the report noted. The Fynbos and Succulent Karoo Biomes will become drier, savanna-like, and more woody, and extinction risk is likely to increase.
Rising sea levels, altered fire regimes and extreme weather events threaten infrastructure, livelihoods, air quality and water safety.
“Greenhouse gas reductions and biodiversity-friendly renewable energy remain important mitigation strategies …. Well-managed ecological infrastructure — including wetlands, rivers, estuaries, coastal dunes and kelp forests — can protect communities, support resilient agriculture and maintain water supply,” the report says.
Wildlife crime measures failing
Between 2010 and 2023, about 9 500 southern white rhinos were poached. Tens of thousands of cycads, 71% threatened, have been illegally harvested from wild populations, even in protected areas, in the past 30 years.
A “lack of effective guardianship” of endangered abalone has seen an estimated 90% reduction in abundance over the past 35 years. The West Coast rock lobster has been reclassified from Least Concern to Endangered, largely due to illegal fishing.
Official seizures and online trade data show that reptiles, medicinal plants, seahorses, pipefish, sea cucumbers, marine gastropods, fish maw, and live ornamental species, including sharks, rays and corals, are being targeted.
Since 2020, illegal harvesting of ornamental succulent and geophytic plants, in high demand in Europe and Asia, has seen a dramatic escalation in the Succulent Karoo Biome, where “range-restricted endemic plant species are easily accessible, and local people have limited livelihood opportunities”.
More than 1.1 million harvested plants have been confiscated, 632 species populations are in decline, and the populations of 12 endemic species have been reduced to functional extinction.
Addressing the illegal wildlife trade through conventional law enforcement, focused on stringent legislative measures such as trade prohibitions, is failing, the report said.
“Despite substantial enforcement, policy and management efforts directed towards curbing the poaching of rhinos, many have been killed within state-owned protected areas, leaving the private sector with the responsibility of protecting just over half the national herd,” it said.
“Similarly, 96 million South African abalone have been poached in 10 years, despite a severely reduced catch limit for the legal fishery.”
Many comprehensive response strategies and management plans—particularly for cycads and succulents—are severely under-resourced and poorly implemented. Conservation agencies lack the resources to implement effective compliance measures.
Legal trade offers a “new frontier” for addressing wildlife crime by supplying persistent demand, while directly tackling socio-economic challenges and generating funds for conservation.
“Molecular techniques, such as DNA and stable isotope forensics, as well as the use of artificial intelligence, 3D printing and other accessible digital technologies that improve monitoring, training and databasing, provide innovative technological solutions for ensuring that trade is well-regulated and does not threaten wild populations.”
Rising extinction risk
Extinction risk is increasing across reptiles, birds, mammals, and plants, according to the report. Freshwater birds are being classified into higher threat categories due to pollution and habitat degradation, while climate change and habitat loss from mining and renewable energy are driving declines in mammals, plants, and reptiles.
Many plant species uplisted for higher extinction risk are in the drought-hit Northern Cape, where pressures from mining, succulent poaching and energy developments continue to intensify.
Freshwater and cartilaginous fishes are most at risk, with sharks, rays, and chimaeras declining due to overfishing, bycatch, lethal shark control programmes, and habitat degradation.
Half of South Africa’s freshwater fish species are endemic, particularly in Western Cape river systems, and “with river health deteriorating and limited resources for conservation action, their status is expected to continue declining”.
Up to 66% of freshwater fish taxa are now threatened, driven by invasive alien fish and habitat modification, with more than 100 species shifting from least concern to threatened categories.
The report also notes that the iconic Brenton blue butterfly has “likely gone extinct” due to high fuel loads from invasive plants and climate-linked intense wildfires.
Habitat loss, degradation
Ecosystem service delivery is declining. Expanding settlements and croplands resulted in annual habitat loss exceeding 100 000ha between 1990 and 2022, although rates have been slowing.
Freshwater and estuarine areas face pressures from mining, agriculture, and housing, compounded by reduced flows and pollution.
Marine biodiversity is affected by coastal and offshore mining, oil, and gas extraction. Sustainable planning can prevent biodiversity loss while supporting economic growth.
Invasive species continue to spread, with three new alien species detected per year since 2018. Invasive plant coverage increased by 10.6% between 2008 and 2023, affecting 17% of terrestrial ecosystems. Biological invasions account for 31% of threatened terrestrial ecosystems and 36% of threatened species, reduce water availability, and cost R340 million annually in livestock productivity.
Rivers, wetlands, groundwater, estuaries and marine ecosystems are key to the country’s water and food security, yet they are increasingly degraded by widespread pollution, the report said.
A third of aquatic ecosystems are now in poor condition, and half of estuaries face moderate to very high pollution levels.
Pollutants from agricultural runoff, failing wastewater treatment works, leaking sanitation networks, unmanaged stormwater and industrial activities, rural and peri-urban solid waste “disrupt the functioning of terrestrial, freshwater and coastal ecosystems, triggering oxygen depletion, eutrophication, die-offs of aquatic species and the spread of invasive plants”.
Emerging contaminants such as microplastics, pharmaceuticals and persistent organic pollutants, including PFAS and legacy pesticides like DDT, “are now being detected from Lake Sibaya [in the iSimangaliso Wetland Park] to offshore coral reefs”.
The report noted that as aquatic systems have limited capacity to absorb this pollution, “water quality is deteriorating to the point where it threatens public health, undermines access to safe drinking water and reduces the availability of clean water for food production and other economic uses.”
Meanwhile, more than 20% of estuaries suffer severely reduced freshwater input, and nearly a third face severe pollution pressures. Only 62 rivers reach the sea without major barriers, weakening land-sea connectivity, threatening fish nurseries, sediment transport and species dependent on both freshwater and marine environments.