The rains have come. Streets are submerged, drains are overwhelmed, and water is everywhere. Then the floods recede — and life slowly tries to return to normal. You turn on your tap or pump your borehole, relieved that the water is flowing again.
But is it actually safe?
This is one of the most dangerous assumptions made after flooding in Nigeria. Floodwater does not simply pass through — it leaves something behind. And what it leaves behind in your water sources can make you very sick.
What Floodwater Actually Carries
Floodwater in Nigerian cities and towns is rarely just rainwater. By the time it reaches your compound, it has swept through streets, open drains, dumpsites, pit latrines, and sewage channels — picking up everything along the way.
Research published in Applied Water Science confirms that flooding increases faecal indicator bacteria counts in groundwater sources during and immediately after flood events. In simple terms: floodwater carries faecal matter, and it finds its way into wells and boreholes.
The specific contaminants introduced include:
Bacteria such as E. coli, Salmonella, Shigella, and Vibrio cholerae — all capable of causing severe illness. A study assessing water sources in Ibadan found E. coli and Salmonella in wells and boreholes, with contamination significantly higher during the wet season.
Parasites such as Giardia lamblia, Entamoeba histolytica, and Cryptosporidium — which cause persistent diarrhoea and stomach illness and are harder to kill than bacteria.
Chemicals from flooded dumpsites, fuel stations, agrochemical stores, and industrial areas — including heavy metals, pesticides, and petroleum compounds that boiling alone cannot remove.
Sediment and debris that clouds the water and provides hiding places for pathogens, making it harder to treat effectively.
This is not a theoretical risk. It has direct, measurable consequences for Nigerians every single rainy season.
The Cholera Connection
The link between flooding and cholera in Nigeria is well-documented and deeply alarming. In 2024 alone, Nigeria reported over 10,837 cholera cases and 359 deaths across 35 states and the FCT, according to WHO data — with the outbreak triggered and worsened by flooding across the country.
Save the Children reported that Nigeria’s cholera fatality rate reached 2.9% in October 2024 — nearly three times the 1% international standard. Children under five were among the most affected.
A review published in Frontiers in Public Health notes that cholera outbreaks in Nigeria consistently peak between June and September — exactly when the rainy season and floods are at their most intense. Flooding overwhelms water systems, contaminating drinking sources with Vibrio cholerae from sewage and waste, creating conditions for rapid transmission.
Water scarcity and water quality are two sides of the same coin. Poor water quality directly or indirectly implies water scarcity. The dumpsites and chemical stores that floodwater sweeps through add a toxic dimension to an already dangerous situation. This further worsens the quality of an already poor water quality in some cases.
Why Wells and Boreholes Are So Vulnerable
Many people assume that boreholes are safe from flooding because they draw water from underground. This is only partially true.
A study on borehole water quality in Port Harcourt found that boreholes in flood-prone and densely populated areas showed significant microbial contamination. The routes of entry include:
- Damaged or loose well caps that allow floodwater to pour directly into the casing
- Cracked well casings that create pathways for contaminated surface water
- Saturated soil around the borehole that carries pathogens downward into the aquifer
- Old or rusty pipes in the distribution system that allow bacteria to enter, as highlighted in our earlier piece on pipeline leakages
Shallow hand-dug wells are the most vulnerable of all — often directly exposed to surface water during flooding. Research in Lagos confirmed that shallow wells showed the highest contamination levels, with contamination significantly worse during periods of heavy rainfall.
Deeper boreholes with intact casings and proper sealing offer more protection — but even these are not immune if the infrastructure around them has been compromised.
Signs Your Water May Be Contaminated After a Flood
Your water may not look or smell different, but watch for these warning signs:
- The borehole or well was submerged or surrounded by floodwater
- The well cap or casing was visibly damaged, displaced, or loose
- The water appears cloudier or has a different colour than usual
- There is an unusual smell — earthy, chemical, or sewage-like
- Multiple people in the household or community fall ill with diarrhoea or vomiting shortly after using the water
- The flood passed through areas with dumpsites, pit latrines, or fuel stations nearby
If any of these apply, treat your water as contaminated until confirmed otherwise.
What to Do — A Practical Step-by-Step Guide
Step 1 — Stop using the water immediately for drinking and cooking. Do not assume floodwater-affected sources are safe. Use stored bottled water, sachet water or water from a known clean source as your first priority.
Step 2 — Let the floodwater fully recede before assessing your source. Do not turn on the borehole pump while the surrounding area is still flooded — this can pull contaminated surface water into the system.
Step 3 — Inspect the physical condition of your well or borehole. Check for a damaged casing, displaced cap, sediment inside the casing, or visible debris. If structurally damaged, call a licensed borehole technician before use.
Step 4 — Flush the system. Once floodwater has receded and the structure appears intact, run the pump for an extended period to flush out the immediate post-flood water before attempting treatment.
Step 5 — Boil your water. According to the CDC, boiling is the most reliable method for killing bacteria, viruses, and most parasites. Bring water to a vigorous rolling boil for at least one full minute, then allow it to cool in a covered, clean container before use. Boiling works for biological contamination — but will not remove chemicals, heavy metals, or fuel.
Step 6 — Chlorinate if boiling large volumes is not practical The US EPA recommends using regular unscented household bleach (sodium hypochlorite, 5–8%) for emergency disinfection. For clear water, add 6 drops per litre. For cloudy water, first strain through a clean cloth, then add 12 drops per litre. Stir and let stand for 30 minutes before use.
Step 7 — Filter before you treat. If water is visibly cloudy or turbid, strain it through a clean cloth or fine filter before boiling or chlorinating. Turbid water blocks the effectiveness of both methods — particles shield pathogens from heat and chemical treatment.
Step 8 — If you suspect chemical contamination, do not boil. Water that smells like fuel, has an oily sheen, or comes from an area where chemicals were stored or flooded should not be used at all. Boiling concentrates chemicals — it does not remove them. Find an alternative source and seek professional assessment.
After Treatment — Storage Matters Too
Treating your water carefully and then storing it in a dirty container or an open bucket undoes all the effort. Store treated water in clean, covered containers. Do not dip unclean hands or cups directly into stored treated water — use a clean ladle or tap.
Prevention — What You Can Do Before the Next Flood
- Raise your wellhead — boreholes and well casings should sit above the typical flood level of your compound
- Seal your well cap properly — a tight, secure cap is one of the simplest and most effective barriers against contamination
- Store clean water before the rains peak — fill clean containers during dry periods as a reserve
- Know where your nearest safe water source is — churches, schools, or community water points may have safer supply during emergencies
- Never locate a borehole near a pit latrine or dumpsite — they should be at minimum 30 metres apart, as public health guidelines recommend
Conclusion
Flooding does not end when the water drains away. It leaves behind a contamination problem that is invisible, odourless, and life-threatening — particularly for children under five, who are the most vulnerable to the waterborne diseases that follow.
The good news is that practical, low-cost steps can protect your household. Boiling, chlorination, proper storage, and basic borehole maintenance are not complicated. They simply require awareness — and that is exactly what this article is for.
When the floods come this year, do not just ask whether the water is flowing. Ask whether it is actually safe.
For more on Nigeria’s water challenges, read up on
Jay water advisory 