How Kenya's Flooding Season Contaminates Your Drinking Water

During the long rains, surface runoff carries agricultural chemicals, sewage and sediment into reservoirs and boreholes. Contamination peaks within 48 and 72 hours of heavy rainfall.

Why Flooding is a Water Quality Emergency

Kenya experiences two distinct rainy seasons, the long rains (March–May) and the short rains (October–December). Both bring intense downpours that routinely overwhelm municipal drainage systems and water treatment works. When flood water flows across farmland, settlements and industrial areas before reaching rivers and reservoirs, it carries a heavy load of contaminants.

The 2023 El Niño floods caused at least 31 counties to report elevated turbidity in municipal water supplies, prompting WASREB to issue advisories for residents in Kisumu, Nakuru and parts of Nairobi to boil water before drinking.

Source: WASREB Flood Advisory Update, November 2023.

The Four Main Contaminants Introduced by Flooding

Are Boreholes Affected?

A common misconception is that boreholes are protected from surface contamination. In reality, poorly sealed borehole casings allow flood water to short-circuit down the annular space between the casing and the borehole wall. Research conducted in Kiambu County showed that coliform counts in shallow boreholes increased by an average of 340% during the first week after heavy rainfall events.

Source: Groundwater contamination during flood events, Kiambu County study.

What Your Municipal Supplier Does, and Where the Gaps Are

Nairobi Water and Sewerage Company and county utilities increase chlorine dosing during high-turbidity events. However, high sediment loads can bind with chlorine, reducing its effectiveness, and treatment plants can be overwhelmed during extreme events, leading to partially treated water reaching households.

• Turbidity above 4 NTU makes chlorination significantly less effective (WHO guideline: <1 NTU for treated water).
• Flooding can dislodge biofilm in distribution pipes, releasing bacteria into the supply.
• Pressure drops caused by burst mains allow back-siphonage of contaminated water.

How to Protect Your Household During Rainy Season

• Continue running your RO purifier, it handles both biological and chemical contaminants.
• Replace sediment pre-filters promptly after a major flood event; they clog faster during high-turbidity periods.
• If you rely on a tank, cover it securely and avoid using it for the first 24 hours of a flood event to allow sediment to settle.
• If you experience a notable change in taste, colour or odour during rains, contact your purifier service provider to check your system.

Q: Should I stop using my borehole during heavy rains?

A: You should increase monitoring frequency. Have a water quality test done within 72 hours of any significant flood event on your property.

Q: Will boiling alone make flood-contaminated water safe?

A: Boiling kills most bacteria and viruses but does not remove nitrates, pesticides or sediment. RO filtration addresses biological and chemical contaminants together.

Stay safe through every rainy season

iClear's multi-stage purifiers handle surges in turbidity, bacteria and chemical load. Find out more.