Concerns over R15-million plan for Milnerton Lagoon

A pilot project by the City of Cape Town will take groundwater from below the Milnerton beach and add it upstream of the lagoon. Photo: Abonge Chiya

• Water quality in Milnerton Lagoon has improved since 2024, according to City of Cape Town data.
• But a UCT scientist and residents say the sources of pollution, including the Potsdam sewage works, have not been dealt with.
• Critics say the City’s R15-million pilot to pump salt water into the lagoon only dilutes the pollution and sends it out to sea.

The Milnerton Lagoon is starting to recover after years of pollution. But a residents’ association and a University of Cape Town (UCT) scientist say the sources of the pollution have still not been fully dealt with.

UCT’s professor Kevin Winter said the City’s water quality data show some improvement since 2024. This includes fewer bacteria, less chemicals such as ammonia, nitrogen and phosphorus, and less chlorophyll.

“There is evidence of some improvements in 2026 and in some instances, the lagoon water quality at Woodbridge Island Bridge is getting closer to the better-quality water that was evident in 2018,” he said.

The Milnerton Lagoon has been heavily polluted for years, mostly by poorly treated effluent from the Potsdam Wastewater Treatment Works. The works releases more than 40 million litres of effluent a day into the Diep River, about 5km upstream of the lagoon.

According to data by the Department of Water and Sanitation, Potsdam failed to meet national effluent standards since 2018.

Other sources of pollution include stormwater from the nearby Joe Slovo informal settlement and the Montague Gardens industrial area, sewer pipe collapses and pump station overflows, sediment and fertiliser from farms in the upper catchment.

Winter said the water will need more time to improve. Some of the best signs of this will be clear water and a greater diversity of fish and bird life.

But the main causes of pollution still need to be dealt with, he said.

A screenshot from the City of Cape Town’s Inland Water Quality Dashboard shows how E. coli levels have improved since 2024. But E. coli is most often above the acceptable limit.

Caroline Marx, who heads the environment portfolio of the Milnerton Central Residents Association as well as Rethinkthestink, said it is too early to celebrate.

“In 2026, there have been repeated serious sewage pollution events, with Potsdam Wastewater Treatment Works again releasing tens of millions of litres per day of shockingly poor-quality effluent despite years of assurance that performance was improving,” said Marx.

On 8 September, E. coli at the Woodbridge was recorded at 141,000 colony-forming units (cfu)/100ml. E. coli must be below 4,000 cfu/100ml for canoeing to be safe. E. coli levels stayed above this unacceptable risk threshold for at least a month.

She called September’s reading “deeply disappointing”. It comes six years after the Green Scorpions issued the City with a directive to address the pollution.

The most recent E. coli reading, on 20 October, shows 1,600 cfu/100ml, categorised as an “acceptable risk”. But levels of nitrogen, ortho-phosphate, and un-ionised ammonia were at unacceptable levels.

Marx said there were encouraging signs of recovery after the heavy rains in 2025. The sewage smell disappeared, seagrass began to regrow, and large schools of fish returned. But a cleaner-smelling lagoon does not mean the underlying pollution problem has been solved, she said. After six years of directives and repeated assurances, the public should not have to rely on heavy rain to clean the lagoon.

R15-million pilot project

The City of Cape Town has launched a R15-million pilot project to dilute pollution in the lagoon by extracting saline groundwater from the beach and adding it to the upper lagoon.

Winter called it a “bold experiment” will raise dissolved oxygen and salinity in the lagoon and flush pollutants out to sea. But it does not try to deal with the sources of the pollution, and once again the sea will receive the pollution, he said.

“Dilution of pollution is not the solution,” said Winter.

In a statement in September, deputy mayor Eddie Andrews said drilling the well points for the pilot would take two weeks, and water would be added to the lagoon in early October. A six-month trial would follow, during which water quality and environmental conditions would be closely monitored. The results would show whether the project should continue, be changed or be stopped, he said.

The City said the project is being carried out under a directive issued under section 28(4) of the National Environmental Management Act.

Asked about the environmental impact of putting salt water into the lagoon’s fresh water, Andrews told GroundUp: “Milnerton Lagoon is a tidal system, and saline water intrusion into the lagoon has previously been recorded as far upstream as the Otto du Plessis Drive Bridge. The pilot is therefore being implemented with consideration of the lagoon’s existing saline conditions.”

An aerial image from November 2022 shows polluted black water flowing into the ocean. Photo supplied

Potsdam upgrade

Mayco member for water and sanitation Zahid Badroodien told GroundUp the pilot project “does not detract from the City’s substantial investment in wastewater infrastructure, including the R5.2-billion upgrade of the Potsdam Wastewater Treatment Works, as well as ongoing sewer and pump station upgrades”.

“The Potsdam upgrade, which commenced in April 2023, remains under construction. While the partial upgrade may be contributing to some of the observed improvements, other factors, including rainfall, tidal exchange, lagoon-mouth conditions, sewer overflows, and stormwater inflows, continue to influence water-quality results,” he said.

In October, new 65-million-litre-a-day membrane bioreactor filters were installed at Potsdam. The City said the upgrade was 80% complete.

Mayor Geordin Hill-Lewis said in a statement the upgrade will more than double the plant’s capacity, from 47 to 100-million litres a day, and the full upgrade will be completed next year.

“I’m also encouraged to see how the ongoing upgrade is already contributing to improved environmental health at the Milnerton Lagoon,” said Hill-Lewis.

Winter said the upgrade at Potsdam has been a major contributor to the improvements in the lagoon, but it is not the only source that needs attention. The Diep River catchment starts in farming areas in its upper course, where sediment and fertilisers could be causing pollution, he said.

Marx said other infrastructure projects, including the upgrade of the Phoenix Pump Station, need to be sped up. The lagoon has shown that recovery is possible, but it will not last unless pollution is stopped at source, she said.

Marx is also worried about a plan to dredge the lagoon. “Redistributing dredged material within the lagoon rather than pumping it out to sea or removing it off site does not guarantee a long-term environmental benefit and could create large mudflats on either side of the proposed channel, potentially changing the beautiful character and appearance of the lagoon,” said Marx.

The City did not answer GroundUp’s question about the status of the dredging plan. In July, it said environmental authorisation for dredging had been granted, but eight appeals had been lodged. A decision was expected later this year. If the authorisation is upheld, dredging is expected to start in early 2027, the City said.

Support independent journalism
Donate using Payfast