Sewage and Pollution in the Diep River Estuary and Milnerton Lagoon - 12 Feb 2026
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| Graphic Illustration Only |
Milnerton Lagoon Pollution Report up to 12 February 2012
"The Diep River and Milnerton Lagoon (including Woodbridge Island) in Cape Town have become notorious for chronic sewage pollution. In recent years local residents, scientists, and journalists have documented repeated sewage spills, foul odours, and ecological collapse in this estuarine system[1][2]. The lagoon is the final reach of the Diep River (Rietvlei Wetland downstream) as it enters Table Bay by Lagoon Beach. It historically supported diverse bird and fish life and recreational use, but today it is heavily degraded. For example, despite official commitments to clean it up, the lagoon “remains in a chronic state of environmental degradation” characterized by persistent sewage and nutrient pollution[2]. A City of Cape Town monitoring report found that Milnerton Lagoon was “mostly in an unacceptable condition” for recreation and that its water “would probably have posed risks to human health most of the time”[3]. This report examines the latest (up to early 2026) accounts of pollution in the Diep–Milnerton system: its sources, environmental and health impacts, and efforts to clean up and manage the crisis.
The overwhelming
driver of pollution is untreated or poorly treated sewage entering the Diep
River upstream of the lagoon. Cape Town’s main treatment works in the lower
Diep catchment – the Potsdam Wastewater Treatment Works – is cited as a major
culprit. Groundwater and official data show that Potsdam has frequently failed
to meet discharge standards. For example, over 2024 it met the minimum effluent
guideline on only 3% of monthly tests, with ‘bad’ chemical and physical
compliance scores[4]. City data indicate
that immediately downstream of Potsdam the lagoon receives E. coli counts in
the millions (7.3×10^6 cfu/100mL in one November 2024 test) versus only
2.9×10^4 cfu/100mL upstream of the works, implicating the plant as a pollution
source[4][5]. City and NGO
commentators note that during summer the lagoon’s main fresh-water inflow
(40–47 ML/day) is essentially Potsdam’s effluent, which “would not result in
pollution if the [WWTW] was properly treating the sewage it receives”[6][4]. In 2023 Cape Town
began a R5.2 billion upgrade of the Potsdam works (doubling capacity from 47 to
100 million L/day) to improve treatment; completion is scheduled for 2027 (with
trials in 2026)[7][4]. However, work delays
(appeals, appeals, procurement) have led to official extensions of the deadline
to the end of 2027[8]. In the meantime,
failures at Potsdam – and in the connected sewer network – continue to foul the
lagoon.
Besides Potsdam, the Diep catchment has numerous failing sewage pipes
and pump stations. In 2024 the City reported multiple sewer-line collapses
(July–Sept) which dumped raw sewage into stormwater drains feeding the lagoon[9][10]. Major pump stations
(e.g. Koeberg Road, Greyville) have also overflowed or broken down, especially
during load-shedding power cuts. For instance, local volunteers noted raw
sewage spilling near Woodbridge Island and Milnerton after a greywater pump
failure[11]. Stormwater
infrastructure itself often acts as a conduit for pollution: heavy rains and
flooding flush litter, hydrocarbons, and faecal waste from informal settlements
directly into the river system[12][13]. Many older suburbs
lack adequate sanitation, with illegal connections between sewer and storm
drains exacerbating contamination (especially in slums)[12]. One analysis warns
that stormwater channels “function as a conduit for pollution rather than a
protective system”[12]. Informal settlement
run-off (failing sewerage, buckets) and overflowing community pit toilets are
repeatedly cited as adding to the sewage load[14][15]. In summary, multiple
urban sources – an overloaded treatment plant, broken pipes and pumps, and
sewage-laden storm drains – conspire to dump billions of litres of raw or
semi-treated waste into the Diep River upstream of the lagoon.
Other pollution inputs include urban and industrial runoff and litter. The estuary also receives trash (plastics, tyres) washed down from the city. A 2025 environmental study found moderate microplastic contamination in Diep River waters and sediments, dominated by polyethylene fibres. Importantly, the highest microplastic counts were detected near a wastewater treatment works (site DR-4)[16]. This suggests that sewage effluent is carrying microplastics into the system. Overland runoff carries industrial chemicals and nutrient fertilizers from upstream industrial zones and agriculture, further fuelling algal blooms. In short, sewage is the dominant pollutant, but it is compounded by urban debris and chemical runoff.
Environmental and Health Impacts
The
pollution has devastated the estuary’s ecology. Sightings of dead fish, foul
foam, and algal mats are common. For example, mass fish kills were documented
in 2022: hundreds of mullet (Liza richardsoni) washed up in March 2022
after a sewage spill, and again in October 2022 during an intense foul-smell
period[17]. The city
attributed these kills to algal blooms depleting oxygen, a classic
eutrophication effect of nutrient-rich sewage[17]. By late
2024 residents described the water as “toxic” and “dead,” with native fish and
sensitive invertebrates largely gone[18][19]. A
city-affiliated survey noted that the lagoon was an important nursery for
west-coast species (e.g. Cape stumpnose, white steenbras)[20] – yet this
nursery function has been undermined by pollution. Birdlife has also shifted:
while opportunistic species (e.g. ibis, cormorants) remain, flamingos and
waders visit far less often than before. Pollution bioaccumulates through the
food chain, threatening long-lived piscivores like herons and ospreys[21].
Algal blooms and foul odours are now routine. Red-green algal scum or
foam often coats the lagoon’s surface. The rotting vegetation and sewage
produce hydrogen sulphide (H₂S) gas (“sewer gas”) that smells like rotten eggs.
Neighbours report waking at night to “eye-watering,” nauseating odour wafting
from the water[1][22]. One
Canyon Drive resident told media the stench was “nauseating” in recent weeks,
yet City officials have mostly blamed infrastructure failures, while
culpability data points to Potsdam’s effluent[22]. The
pungent odour has prompted repeated public-health warnings. A City sign on the
Woodbridge Island boardwalk now reads: “Polluted water: for health reasons,
swimming and recreational activities are at your own risk.”[23]. Canoeing
and fishing groups have suspended activities: the Milnerton Canoe Club reports
that paddlers who once enjoyed the lagoon have abandoned it, calling the water
“toxic” and “progressively worse”[19].
Public health experts warn of real risks. Sewage-laden water contains
high counts of faecal bacteria (E. coli, enterococci) and viruses. Repeated
testing by citizen science teams (Project Blue/Rethink the Stink) found
dangerously elevated bacteria at Milnerton and nearby Blue-Flag beaches in late
2024[24]. The
City’s own studies show bathing in these waters would be “unsafe for
full-contact recreation”[25].
Veterinarians report dogs falling ill after swimming or drinking lagoon water
(vomiting, diarrhoea, even deaths). Local doctors say residents suffer frequent
sinusitis, irritated eyes, headaches and asthma flares traced to the odour[26]. Hydrogen
sulphide is a potent irritant and can trigger bronchitis or worse in susceptible
people. For example, Dr. Michelle Maartens of Milnerton noted patients with
chronic nasal irritation when smelly lagoon conditions prevailed[26]. Community
groups argue that chronic low-level H₂S exposure – plus periodic spikes over
200 ppb – may be harming lung health, especially in children and the elderly[27][28].
Air quality monitors were vandalised but reinstated in 2025, showing 24‑hr H₂S averages within WHO guidelines[29]. However, activists point out these averages mask odour episodes: H₂S is heavier than air and tends to pool near the ground, yet the City’s monitor sits 3.5 m high[27]. In practice this may understate real exposure. CAPEXIT councillor Bodin reports residents “still experiencing the same toxic odour… nasal and airway issues with wheezy lungs” long after enforcement began[30]. In summary, the lagoon’s sewage pollution has created a persistent ecosystem and public-health hazard.
Mitigation and Clean-up Efforts
Cape Town
authorities have implemented multiple mitigation projects, but the scale of the
problem means progress has been slow. Upstream infrastructure upgrades are
central. As noted, a R5.2 billion expansion of the Potsdam sewage works is
underway (to be completed ~2027) to drastically reduce overloaded effluent.
Pumps and pipes are being upgraded as well. For example, the Koeberg Road pump
station upgrade was extended out to 2025 and its secondary phase to 2028 under
provincial directives[31]. The city’s
long-term plan also includes dredging the lagoon itself to revive tidal
flushing. In early 2026 an official environmental assessment proposed dredging
the channel from the Loxton Road bridge to the estuary mouth[32]. The stated
aim is to “reshape the channel profile and enhance tidal exchange,” drawing
more oxygenated seawater into the lagoon and creating raised mudflats to aerate
sediments[33]. This
dredging (if approved) would complement structural fixes by improving natural
cleansing.
Several targeted engineering interventions aim to cut off sewage
inflows. The city has identified and started on projects in the Diep catchment
to divert or filter stormwater. For instance, runoff from Dunoon/Doornbach is
being routed into the sewer system with new gravity lines leading to Potsdam
WWTW, instead of directly into the river[34]. Litter
traps and constructed wetlands have been built on Erica Road and the Theo
Marais canal to capture pollutants and low flows before they enter the lagoon[34]. (Indeed,
volunteer teams still regularly clear debris from the Theo Marais canal to
remove sewage sludge.) Another project diverts stormwater from informal
settlements (Joe Slovo, Phoenix) into sewer pipes after screening, rather than
dumping raw flow into the river[34]. All these
stormwater-bypass schemes were completed by late 2022 and are now being tested.
The City has also beefed up monitoring and response. In 2025 it
expanded continuous air-quality monitoring at Woodbridge Island, and it
maintains public “Pollution” dashboards online. Wastewater pump stations are
equipped with telemetry to alert staff of overflows, and crews patrol storm
drains during rains to fix illicit connections. Officials say they conduct
frequent water sampling and use GPS tracking of trucks pumping out emergency
sewage overflows[35]. Signage
around the lagoon now warns against swimming, and public press releases
emphasize vigilance. In June 2025 the Western Cape minister reported that the
city had been “addressing sewer line collapses and other infrastructure
failures” and “installing litter nets and telemetry systems” under emergency
directives[35]. The city
also appointed a specialist ecologist to oversee the Diep/Milnerton
rehabilitation plan[36]. These
measures – often mandated by provincial “Green Scorpions” directives (see
below) – represent short- and medium-term fixes while major works continue.
Citizens and NGOs have played a watchdog role. The volunteer group Rethink the Stink (Milnerton Central Residents Assoc.) regularly tests lagoon and sea water and publicizes results. In late 2024 Rethink published “Project Blue” data showing dangerously high faecal bacteria at Camps Bay and Clifton beaches, challenging official claims of clean oceans[24]. Similarly, surf club lifeguard Jamii Hamlin and UWC researcher Jo Barnes have taken samples at the lagoon mouth to hold authorities accountable. Other activists (including OUTA) have petitioned courts and councils for faster action. In January 2025 a local resident even defaced a road sign on Woodbridge Island (changing it to “Diepk@k”) to protest the “ongoing stench”[37] – a vandalism that brought media attention to the issue. These community efforts have pressured the City to be more transparent: for instance, the mayor’s office now publicly shares status updates on Potsdam and lagoon projects.
Official Oversight and Reports
Several
official reports and data streams document the crisis. Most prominently, Cape
Town’s annual inland water-quality report has flagged the Diep/Milnerton system
for special attention. The 2023/24 report noted that the proportion of river
sites failing safety criteria rose from 49% in 2019 to 59% in 2023, largely due
to more load-shedding and unserved settlements[13]. It singled
out Milnerton Lagoon as an exception: “mostly in an unacceptable condition” in
2023[3]. The report
explicitly identified the catchment “between Blaauwberg Bridge and Otto du
Plessis Drive” – i.e. the lower Diep – as a source of raw sewage, citing
overflows from Potsdam WWTW and local pump stations, plus polluted
informal-settlement runoff[15]. This
data-driven acknowledgement has guided policy: for 2024/25 the City budgeted R2
billion to upgrade treatment works and R1 billion for sewer maintenance and pump
upgrades, aiming to prevent overflows[38].
Provincial authorities have also intervened. In September 2020 the
Western Cape environmental department issued a formal directive (under NEMA)
requiring Cape Town to rehabilitate Milnerton Lagoon[39]. Under this
order, the city must implement specific solutions by set deadlines. After the
city requested more time, the province granted extensions: the Potsdam WWTW
upgrade deadline was pushed back to 31 Dec 2027[8], and the
Koeberg pump station upgrade to 2028[31]. These
shifts drew criticism from activists seeking accountability. In May 2025 the
RethinkTheStink group formally challenged the extensions, questioning why years
were granted when the problems were well known[8].
Provincial legislatures have also questioned progress. In June 2025 the
Western Cape Parliament’s committee meeting published an answer by Minister
Anton Bredell detailing city actions. He confirmed that two directives had
“directly resulted in upgrading existing sewage infrastructure” and listed many
city interventions (sewer repairs, canal clean-ups, specialized monitoring,
etc.)[40]. He noted
the city’s appointment of a “freshwater specialist” to oversee the
Diep/Milnerton rehabilitation[36]. These
public disclosures underscore that the crisis is being tracked at high
government levels.
At the same time, independent scientists have studied the system. A 2025 peer-reviewed study of microplastics found pervasive plastic fibres in Diep River samples, indicating the estuary is not only a biological but also a chemical pollutant sink[41]. Researchers elsewhere have highlighted pharmaceutical and chemical pollutants in the marine outfalls near Milnerton, linking them back to the lagoon’s leaks[42]. These scientific findings (combined with city data) paint a picture of a multi-faceted pollution problem.
As of early 2026
the situation remains precarious. Temporary improvements have been seen – for
instance, some residents reported relief when high tides flushed the lagoon in
late 2024[43] – but chronic
pollution persists. Water quality datasets on the City’s public dashboard show
Milnerton Lagoon’s condition in 2024 was actually worse on average than in 2019
(the year the clean-up directive was issued)[44]. Beach warning
signs and odour alerts remain in place. Many local people remain sceptical: as
one resident put it in January 2025, “I always read about all the interventions…
yet [the stench] is still there”[45].
On the positive side, significant funding and projects are committed
for the coming years. Tens of millions are being spent on sewer diversions and
pumps, and the Potsdam upgrade – once complete – should greatly reduce the
effluent load. The proposed lagoon dredging (currently undergoing environmental
review) promises long-term ecological benefits by restoring tidal flow. Citizen
groups continue to monitor and publicize conditions, keeping pressure on
officials. Air-quality monitors and health reviews are in place to detect any
dangerous exposure spikes. However, many deadlines have slipped (Potsdam now
2027, pump stations 2028)[8][46], and the
lagoon’s ecosystem remains fragile.
In summary, by 2026 the Diep River–Milnerton Lagoon system is still one of Cape Town’s most polluted waterways. Repeated sewage spills have caused repeated fish kills, noxious odours, and high human-health risks[17][3]. A mix of technical fixes – plant upgrades, pipe repairs, wetlands, and dredging – are underway or planned, backed by official directives and significant budgets[32][38]. Yet the scale of past neglect means the community remains on alert. As one canoe club member lamented: “It’s toxic and stinks to hell” – a state of affairs Cape Town has pledged to resolve but has not yet fully fixed[19]. (Source: Deep Research ChatGPT 5.2)
References
Cape Times. (2024, November 27). Water quality report finds rising
risks from sewage. CapeTimes.co.za. [13][3]
Daniels, K. (2025, January 28). Sign at Woodbridge Island restored after
pollution defacement. TygerBurger. [37][45]
Engel, K. (2023, August 1). City of Cape Town finally launches project
to restore heavily polluted Milnerton Lagoon environment. Daily Maverick.
(via Milnerton Central Residents Assoc.). [7][17]
Jeranji, T. (2019, December 11). Residents tackle City over dirty
lagoon. Netwerk24. [47][48]
Khan, A. B., Pereao, O., Sparks, C., & Opeolu, B. (2025). Assessing
microplastic characteristics and abundance in the sediment and surface water of
the Diep River, Western Cape, South Africa. Environmental Pollution, 381,
126555. [41]
Kretzmann, S. (2024, December 13). Sewage stench lingers at Milnerton
Lagoon. GroundUp. [22][4]
Savage, R. (2025, April 17). Kicking up a stink: row over sewage
pollution blighting Cape Town’s beaches. The Guardian. [1][24]
Swart, M. (2025, December 23). Environmental activists challenge Cape
Town’s air quality claims around Milnerton Lagoon. Cape Argus (IOL). [27][30]
City of Cape Town. (2024). Annual Inland Water Quality Report 2023.
City of Cape Town (summarized in Cape Times)[13][3].
City of Cape Town. (2024, November). Liveable Urban Waterways
Programme – Budget allocation 2024/25. [38].
City of Cape Town, Water and Sanitation Dept. (2022). Improving the
Quality of Stormwater Discharging into the Diep River (internal report; see
comments by MCRA)[48].
Western Cape Government, Environmental Affairs. (2025, June 13). Reply
to question 36 – interventions for Milnerton Lagoon sewage pollution
(Parliamentary reply, Anton Bredell). [35][36]
Rethink The Stink (Marx, C.). (2025, May 12). Letter to WC Minister:
Re Diep River and Milnerton Lagoon directives – extension of timelines[8].
Vernon Chalmers. (2026, January 26). Milnerton Lagoon Pollution Report
– January 2026. vernonchalmers.photography. [2][49].
Sources: Reports and news articles (see above)
from Cape Town media and research, including City of Cape Town releases, NGO
bulletins, and scientific journals[7][3]. All in-text
citations refer to these sources.
[1] [14] [23] [24] [42] Kicking up a stink: row over
sewage pollution blighting Cape Town’s beaches | South Africa | The Guardian
[2] [12] [21] [25] [49] Vernon Chalmers Photography
Training: Milnerton Lagoon Pollution Report – Jan 2026
https://www.vernonchalmers.photography/2026/01/milnerton-lagoon-pollution-report-jan.html
[3] [13] [15] [38] Water quality report finds rising
risks from sewage
https://capetimes.co.za/news/2024-11-27-water-quality-report-finds-rising-risks-from-sewage/
[4] [5] [6] [9] [22]
Sewage stench lingers at Milnerton Lagoon | GroundUp
https://groundup.org.za/article/milnerton-lagoons-ghastly-stench-lingers-on/
[7] [17] [18] [26] City of Cape Town finally
launches project to restore heavily polluted Milnerton Lagoon environment –
Milnerton Central Residents Association
[8] [31] [46] rethinkthestink.co.za
[10] [19] [20] [39] [43] [44] South Africa: Sewage Stench
Lingers At Milnerton Lagoon - allAfrica.com
https://allafrica.com/stories/202412130059.html
[11] Raw Sewage Smell in Woodbridge
Island, Milnerton - Facebook
https://www.facebook.com/groups/stopcoct/posts/2678677522342556/
[16] [41] Assessing microplastic
characteristics and abundance in the sediment and surface water of the Diep
River, Western Cape, South Africa - ScienceDirect
https://www.sciencedirect.com/science/article/pii/S0269749125009285
[27] [28] [29] [30] Environmental activists challenge
Cape Town's air quality claims around Milnerton Lagoon
[32] [33] Proposed Milnerton Lagoon
Dredging - Infinity
https://www.infinityenv.co.za/public/milnertonlagoondredging
[34] [47] [48] Residents tackle City over dirty
lagoon | Netwerk24
https://www.netwerk24.com/city-to-clean-up-its-act-20191210-2
[35] [36] [40] Local Government, Environmental
Affairs and Development Planning | wcpp
https://www.wcpp.gov.za/?q=node/19313
[37] [45] Sign at Woodbridge Island
restored after pollution defacement | TygerBurger
https://tygerburger.co.za/sign-at-woodbridge-island-restored-after-pollution-defacement-20250128/
