Cyanobacteria and government inaction are threatening the country’s water supply

Cyanobacterium structure. (Source: Wikipedia Commons)

21 Mar 2025

Cyanobacteria are probably the most numerous creatures to have ever existed on Earth. They’re good for making oxygen but otherwise bad news for most life forms. Through neglect of our water systems they’re on a feeding frenzy.

Much of South Africa is facing a water crisis, but it’s not just drought or climate change driving the problem. The country’s lakes and reservoirs are increasingly choked by blooms of toxic cyanobacteria – commonly known as blue-green algae – making masses of water untreatable for household use.

The problem is exacerbated by ageing wastewater treatment facilities and poor infrastructure management. But, as will be seen below, the crisis is not inevitable. Effective solutions exist and could be implemented quickly if the political will were there.

Cyanobacteria are microscopic organisms that thrive in hypoxic, nutrient-rich waters, particularly in reservoirs and lakes with high levels of nitrogen and phosphorus. These nutrients, often the result of agricultural runoff and untreated sewage, fuel massive algal blooms that spread across the surface of water bodies, blocking sunlight and depleting oxygen levels.

The result is a catastrophic disruption of aquatic ecosystems and a threat to public health. Drinking or even coming into contact with cyanobacteria-infested water can cause severe health problems, from skin rashes and respiratory issues to liver and neurological damage.

In extreme cases, as seen at Zimbabwe’s Lake Chivero, toxic blooms have rendered entire reservoirs untreatable for human consumption. Experts warn that South Africa’s water sources are heading in the same direction. Official reports reveal massive scale of the waste, pollution and poorly treated water crisis

Read more: New cyanobacteria discoveries point to alarming changes in our already distressed waterways

The failure of government response

For years, water experts and environmentalists have sounded the alarm over the deteriorating state of South Africa’s dams and the looming impact of cyanobacteria. Dave Shackleton, a water treatment specialist now working in the United States and founder and CEO of SIS.BIO, has spent more than a decade advocating modern remediation techniques to address the crisis.

He warns that South Africa’s wastewater treatment plants are failing to manage nutrient discharge, leading to an explosion of cyanobacteria in rivers and major reservoirs such as Hartbeespoort Dam and Roodeplaat Dam.

“There’s no point waiting for weeds and toxic algal blooms to occur,” he says, “then going out to treat them with chemicals or beetles or whatever. That way you just send even more organic biomass down to the sediment to add to the nutrient stockpile that fuels future blooms.”

Shackleton says there are effective solutions in the US that could be applied to South Africa’s water bodies, but his engagement with South African officials has led to little progress.

“I’ve had meetings with the Department of Water Affairs, sent emails to officials and even spoken at conferences where Ministers promised action,” he told Daily Maverick. “But nothing happens. The bureaucratic inertia is staggering.”

The Department of Water and Sanitation disputes this. It says it has made significant progress in monitoring activities, research into cleaner technologies, developing an eutrophication (overgrowth) strategy and remedying issues at Hartebeespoort Dam. It adds that it has been upgrading and modernising many water treatment facilities and has implemented an early warning system for cyanobacteria.

A range of trial cleanups at a number of sites by the Department of Public Works using Shackleton’s company in 2017 found that it brought down cost substantially and in all cases brought treated effluence discharge into compliance with regulated standards.

A recent Daily Maverick report highlighted plans to hold municipal managers accountable for the national sewage crisis, but critics argue that enforcement alone won’t fix the core problem, which is failing infrastructure and an unwillingness to adopt proven remediation methods.

How cyanobacteria moves

Cyanobacterium structure Structure of a cyanobacterium. (Image: Wikipedia Commons)

One of the reasons cyanobacteria are so difficult to control is their ability to move vertically through the water column. Unlike traditional algae, which float, cyanobacteria regulate their buoyancy, rising to the surface during the day to capture sunlight and sinking at night to absorb nutrients from the depths.

This constant cycling means that conventional treatments – such as applying chemical algaecides – often fail to address the root cause of the problem.

Research has shown that cyanobacteria colonies contain an entire microbiome of organisms that further enhance their ability to absorb nutrients. This makes them even more resilient and capable of rebounding after failed treatment attempts. Instead of killing off algae with chemicals, Shackleton argues, the solution lies in restoring the natural balance of the aquatic ecosystem.

The key to combating cyanobacteria, he says, is oxygen. Many of South Africa’s reservoirs suffer from hypoxia – low oxygen levels at the bottom of the water body. This lack of oxygen triggers chemical reactions in the sediment, releasing more phosphorus and nitrogen into the water and feeding the next wave of cyanobacterial blooms. Over time this sediment can raise the floor of dams, massively, decreasing their water-carrying level.

Shackleton’s company developed a simple and cost-effective method to fully oxygenate them, preventing this cycle from repeating. Once the water is properly oxygenated, beneficial algae and zooplankton outcompete cyanobacteria, reducing its dominance naturally.

“The solution isn’t complex,” Shackleton says. “We need to stop treating the symptoms and fix the root cause. That means increasing oxygen levels, restoring the food web and using biological methods to break down excess organic material at the bottom of these reservoirs.”

The approach, he says, has already yielded success in the US, where projects in Missouri, Colorado and Virginia have transformed struggling lakes and reservoirs. “In some cases, water quality improved so significantly that local water treatment plants were able to cut their use of chlorine and other chemicals in half, reducing the production of harmful disinfection byproducts.”

What this process cannot do, however, is the removal of toxic chemicals or heavy metals contained in domestic/industrial effluent overflowing into the environment from broken or dysfunctional wastewater treatment works. And, of course, oxygenation treats the symptoms not the root causes such as the high volume of organic nutrients (poo), residual chemicals and heavy metals pouring out of collapsed municipal treatment works into rivers and soils.

A private sector solution?

One of the most promising aspects of reoxygenation, however, is its potential for rapid implementation. Shackleton estimates that if allowed to proceed, his team could make 500 megalitres a day of additional water available to Gauteng – water that exists but is unusable because of pollution. This would be equivalent to bringing a major new dam online, without the massive construction costs and environmental impact.

However, he says, the South African government remains reluctant to permit private sector involvement in water management. Political concerns, bureaucratic red tape and vested interests have kept effective solutions on the sidelines while the crisis worsens.

“There’s a lot of talk about bringing in the private sector to help,” he says. “But at the municipal level, there’s no accountability. The money collected for sewage treatment isn’t reinvested in infrastructure. It’s just another revenue stream for struggling municipalities.”

A shift towards privatised water treatment contracts could be one way to cut through the deadlock. The Treasury has already explored the idea of transversal contracts, which would allow government entities to bypass lengthy procurement processes and engage directly with service providers. If properly implemented, this could provide a way to roll out solutions without getting bogged down in political infighting.

Without immediate action, South Africa faces a future in which many of its key reservoirs are too toxic to supply drinking water. The collapse of water security would exacerbate inequality, drive up costs for businesses and households and pose severe public health risks.

Shackleton and other experts argue that the science is clear and that solutions exist. What’s missing is the urgency and political will to act. Until that changes, South Africans can expect their water woes to deepen, with potentially catastrophic consequences for the country’s future. DM

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