The bug in your glass: Why tap water in Nairobi is not so safe

Nairobi
By Kamau Muthoni | Jul 19, 2025

Two weeks ago, I fell ill on a weekend and rushed to the hospital. My symptoms included a painful stomach and acidity.

On Saturday, a day before I got unwell, I had taken some sukuma, pork and ugali at my friend’s house.

At the hospital, we conducted tests, including a  Helicobacter pylori infection test, which is a common stomach infection. However, I was given a clean bill of health.

There was an issue, though, the test results showed that I had symptoms of food poisoning, and traces of bacteria called E. coli.

My doctor asked me if I had taken any water, which jogged my memory that I had brushed my teeth on Saturday night, directly from tap water; I prefer using boiled water for brushing.

For the acidity, I concluded that Sukuma was the suspect while the E. coli, the tap water from the county.

I decided to dig into the quality of water that we take and how the bacteria found their way into my system.

My first point of discovery was a case filed in 2019 by Isaiah Luyara Odado and Wilson Yatta against the National Environment Management Authority (Nema), the Environment Cabinet Secretary, and Nairobi, Machakos, Kilifi, Makueni, and Tana River counties, regarding the cleaning up of the Nairobi River.

Although we do not directly draw water from Nairobi River, Kikuyu Springs is one of the sources of water for Nairobi residents.

Now, Justice Ann Omollo has ordered Nema to test the waters in the Nairobi River after every four months and submit a report to the court.  In addition, it was ordered to coordinate cleaning the Nairobi River from its source to its point of drainage in the Indian Ocean.

Nema’s director, Mamo Boru Mamo, in a report exclusively seen by The Saturday Standard, said that the Nairobi water basin comprises three rivers- Ngong, Nairobi, and Mathare.

The three then join east of Nairobi at Athi River and flow through Machakos, Kitui, Makueni, Kilifi, draining at Sabaki Estuary into the Indian Ocean.

The primary source of water for Nairobi is one of its tributaries called Nyongara stream, which originates at Ondiri. Other tributaries include Kamiti, Ruaka, Karuri, Ruiru, and Kirichwa.

“The Nairobi River originates from Kikuyu, Kiambu County, at Ondiri Swamp. However, the main source has been highly encroached by farming activities and human encroachment,” said Mamo.

However, he says, the rivers are narrow and highly polluted as they meander through the city’s industrial area and informal settlements.

“Water pollution is one of the greatest environmental challenges facing Kenya in recent times,” he said, adding that this is caused by poor waste management systems, informal settlements and encroachment of riparian land, coupled with poor farming activities at the upper catchment areas.

In the report, Mamo singled out Korogocho, Mukuru, and Dandora as the key areas of pollution in the rivers. He was of the view that Nairobi County does not collect the waste at 100 per cent, nor is the waste disposed of at the designated management places.

“Riparian reserves are covered with illegal dumpsites, waste sorting and transfer stations. Leachates from such dumpsites are a source of pollution to surface waters as well as the underground aquifers,” he said.

The Nema boss pointed out that the city is still grappling with dilapidated sewer infrastructure as well as manufacturing industries that had no effective pre-treatment machines.

The other problem identified was that the water treatment facilities are often overwhelmed with waste and become inefficient in treating the received waste before discharging it, resulting in burst sewers and blocked manholes.

Nema conducted water tests in 23 randomly selected sites. It concluded that the water was good for domestic use. However, the environmental conservation body observed that the greatest polluter in all the sites was E-coli, the same bug that had troubled me. It is a type of bacteria that lives in the intestines of humans and animals and causes stomach cramps, diarrhoea, and vomiting.

“The presence of E. coli is evidence of human waste finding its way to the water and resources within the basin,” the report reads in part.

A separate study conducted last year found that the occurrence of E. coli bacteria is increasing in Nairobi, making people sick more often, further cementing the findings by Nema and test results in hospital.

The increase in E. coli is mainly associated with food poisoning, which happens when people consume contaminated water, food, undercooked meat, or unpasteurised milk.

According to the study published in the Proceedings of the National Academy of Sciences, cases of these bacteria are causing drug resistance due to their mobile genetic elements.

It reveals that pathogens are more likely to transfer from animals to humans in densely populated areas.

The study showed that the bacteria is spreading more in areas of Nairobi with high populations of livestock and urban-adapted wildlife, like rats. These areas are often lower-income neighbourhoods with inadequate sanitation and poor waste management.

The study was led by James Hassell, a wildlife veterinarian and epidemiologist, along with Kenyan and United Kingdom partners. They collected E. coli samples from over 2,000 people, livestock, and urban wildlife in 33 locations across Nairobi.

The researchers sequenced all the samples of E. coli, and the bacteria were present in the majority of the samples.

“We can’t redesign urban environments to eliminate the risk of disease spillover, but we want to detect these diseases quickly and minimize their impact. To do that, the focus needs to be on access to quality healthcare that can diagnose and identify new pathogens,” Hassel said.

E. coli bacteria lives in the intestines of humans and animals and causes stomach cramps, diarrhoea, and vomiting. [iStockphoto]

In the meantime, Nema found that septic wells dug along the water sources are leaking into the city’s waters.

Another study by the University of Nairobi’s Department of Veterinary Anatomy and Pathology in 2008 indicated that the Nairobi River, Nairobi Dam, Kabete Dam, and Kawangware Stream had very high numbers of coliform bacteria and E-coli.

“Coliforms and E. coli levels were highest in Nairobi River water samples obtained near Chiromo and Arboretum areas, and lowest in samples obtained at the Museum Hill area. Chunga River along Ngong Road and Mbagathi River had moderately high levels of coliforms and E. coli, and the levels of contamination were still way too high above the World Health Organization (WHO) recommended levels for safe drinking water,” the journal reads in part. It, however, indicated that there was none in tap water and commercial bottled water.

In addition, the use of chemicals and fertilizers in upper catchment areas is identified as another source of pollution as they are washed away into the river water, hence, loading them with nutrients.

“The key sources of pollution identified were discharges from broken or leaking sewer lines managed by Nairobi City Water and Sewerage Company in Nairobi County, Mavoko Water and Sewerage Company, and EPZA sewer lines in Machakos County,” the report submitted in court in compliance with the order read.

On the other hand, Nema officials were dispatched to different locations of the river and took samples for tests.

They tested water from the upper, middle and lower Athi drainage during the wet season. In these areas, they found that the water pH was okay, at 6.94. The allowable limit is between 6.5 and 8.5.

However, the electrical conductivity had exceeded by close to 300 units, as it was 1017, which is above the 800 allowable units.

Queen Mary University of London, in its research journal dubbed Water Quality Indicator: Electrical Conductivity, explains that the presence of charged ions causes the conductivity. The level of conductivity is measured by microsiemens per centimeter (µS/cm) and it helps identify pollution that may harm invertebrates and or fish.

“ Any human activity that adds inorganic, charged chemicals to a river will alter the electrical conductivity. For example, electrical conductivity may be higher in a river downstream of a sewage treatment works due to chemicals,” the journal reads in part.

The World Health Organization (WHO) suggests that water conductivity should be around 300 to 600 µS/cm. WHO, however, says that the levels above 500 µS/cm should be tested but it is not necessarily harmful. Nema’s maximum allowable limit is 800 µS/cm, but in cases where conductivity is above 1000 µS/cm means it is highly contaminated and has the potential to contain lead, mercury, arsenic, chlorides and nitrates, which are harmful to human beings.

At Thika 14 falls, Man Eaters Bridge, and Thwake Dam-Galani inlet, half of the tests done exceeded limits of contamination while at Kathimani- Makutani bridge, only two out of the eight tests, the colour and total suspended solids, exceeded the allowable limits.

As you get closer to Nairobi, the river becomes increasingly polluted. At Waithaka, where Nyangora and Kabuthi meet, electrical conductivity was 1357 while the total suspended solids were 37 against the allowable limit of 30. In addition, turbidity, was 57 against 50, colour was 65.2 times in excess of the allowable limits.

The chemical oxygen and biological oxygen demand were also high, at 163 and 67 against 50 and 30 limits respectively.

However, Zinc, Lead, Copper, Cadmium, Arsenic, and Mercury were undetectable.

At the Bridge near Strathmore School, the electrical conductivity was double the allowable limit with 1877 µS/cm. Further, the total suspended solids were three times the allowable limits, while colour was 89.8 times in excess. At the point, there was detection of Zinc (0.021) and lead (0.01) but they were within the gauge. The allowable limit for the two is 0.5 and 0.01.

Nema also tested the waters at the Museum Interchange. Here, the story of electrical conductivity was the same. It was detected that the water had 1818 µS/cm. The level of Zinc was a bit higher than Strathmore, with 0.24mg/l, while lead was 0.005 mg/l, these too, were within the limits.

The team also tested Kirichwa Kubwa waters. The water was blackish and smelly. Here, the electrical conductivity was 3.5 times higher than the allowable limit while the total dissolvable solids were 1900 mg/l against the 1200 mg/l. The chemical oxygen demand was 47.6 times higher while the biological oxygen demand was 14 times in excess. There was a detection of zinc (0.012 mg/l) but the remainder of the metals were below the detectable limits.

Arboretum waters exceeded the limit in electrical conductivity, total suspended solids, turbidity, colour, and chemical oxygen demand (cod)as set out in the water quality regulations, 2006.

The other point, Michuki Park, the water electrical conductivity was 2027 µS/cm, the colour was in excess by 908 hazen units, while biological oxygen was within limits.

However, the mercury levels at the point were excess, with 0.06 mg/l being detected.

WHO indicates that mercury is corrosive to the skin, eyes and gastrointestinal tract. It may also induce kidney toxicity if ingested.

Of all the 23 points tested, only Ruiru River waters were within the parameters set in the Water Quality Regulations, 2006.

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