Groundwater quality in Africa
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Some general resources for understanding and managing groundwater quality
The quality of groundwater is as important as its quantity: groundwater must be of a suitable quality to make it a useful resource, and poor quality groundwater can also affect surface-water ecosystems. Groundwater quality includes natural chemical variations and the controls on these; and the effects of chemical and microbiological pollution from agriculture, industry and other human activities. Some groundwater quality issues have a long history, such as anthropogenic pollution from nitrate and bacteria from human and animal wastes; increases in salinity from sea water intrusion or irrigation effects; or metal pollution from mining. The natural occurrence of health-harming chemicals in groundwater in some geological environments - in particular, fluoride and arsenic - is known in many parts of the world, including parts of Africa, but may also occur in places as yet unrecognised. Other anthropogenic pollutants are new, such as pharmaceutical chemicals, and are the subject of research around the world, including in Africa.
There are many resources discussing groundwater quality, some in great detail. Some useful overviews include these reports:
- Ravenscroft, Peter and Lytton, Lucy. 2022a. Seeing the Invisible : A Strategic Report on Groundwater Quality. Washington, DC. World Bank.
- This report describes why, and how, groundwater quality is vital to human health, agriculture, industry and the environment.
- World Bank. 2022. Groundwater Quality : A Strategic Approach. Washington, DC. World Bank.
- This policy brief highlights the key messages for policy makers from the World Bank report “Seeing the Invisible: A Strategic Report on Groundwater Quality” (Ravenscroft and Lytton 2022), describing the types of contaminants in groundwater, and techniques to protect the resource from being contaminated in the first place.
- A companion report is a Practical Manual on Groundwater Quality Monitoring (Ravenscroft and Lytton 2022b), which describes tools and resources for groundwater quality measurement and long-term monitoring. More information on groundwater quality monitoring is in the Atlas Groundwater monitoring page.
Drinking water quality guidelines
Where groundwater is used for drinking, it is important that it meets safe standards to avoid damage to human health. The World Health Organisation sets out guidelines for drinking-water quality (2017), which apply to all waters, including groundwater, used for drinking.
Groundwater quality fact sheets
Short, practical fact sheets summarising inorganic groundwater quality in a number of countries have been produced by the British Geological Survey (BGS) in collaboration with WaterAid. These also identify inorganic chemical constituents of risk to health that may be present in groundwater in each country. The BGS have also produced separate fact sheets summarising selected chemical elements that are particularly important to groundwater quality; and some summarising the impacts of selected human activities on groundwater quality. All of these fact sheets can be downloaded from the BGS website at the sites below:
- Download fact sheets for groundwater quality for these countries in Africa: Burkina Faso, Ethiopia, Ghana, Madagascar, Malawi, Mali, Mozambique, Nigeria, Tanzania, Uganda and Zambia.
- Download water quality fact sheets by element for these chemical elements of particular relevance to groundwater: arsenic, fluoride, iodine, manganese and nitrate. These element sheets aim to explain the nature of the health risk for each constituent, the origin and occurrence in groundwater, the means of testing and available methods of mitigation.
- Download fact sheets on the impact of agriculture, industry and urbanisation. These complement the fact sheets on specific groundwater quality parameters and countries, and should be read together with these.

Groundwater contamination and pollution
Groundwater contamination can occur from natural processes - known as geogenic contamination - or from pollution from anthropogenic sources. Some of the main activities that can lead to groundwater pollution are agriculture, industry (including mining) and human waste disposal, but there are many others.
One recent overview of groundwater contamination in sub-Saharan Africa is:
- Masindi, V and Foteinis, S. 2021. Groundwater contamination in sub-Saharan Africa: Implications for groundwater protection in developing countries. Cleaner Engineering and Technology, 2
Geogenic contamination
Geogenic contamination refers to naturally occurring elements that are generally present in groundwater due to dissolution of the aquifer material. Geogenic contaminants in groundwater can have a negative effect on human health, particularly when consumed over prolonged periods of time. The most common geogenic contaminants are fluoride and arsenic. More than 300 million people worldwide are thought to use groundwater contaminated with fluoride or arsenic as a source of drinking water.
- The British Geological Survey fact sheets give an overview of arsenic, fluoride, iodine and manganese, all of which can be geogenic contaminants in groundwater.
- The Swiss Federal Institute of Aquatic Science and Technology (Eawag) has developed a method to assess the risk of groundwater contamination by fluoride or arsenic in a given area, using geological, topgraphical and other environmental data. The Groundwater Assessment Platform (GAP) enables users to upload their own data and generate hazard maps for specific areas. The Groundwater Assessment Platform also hosts a Wiki site where you can find and share information about geogenic contamination, associated health risks, and mitigation options.
Further information on the methodology used by Eawag can be found in these publications:
- Amini, M, Mueller, K, Abbaspour, K C, Rosenberg, T, Afyuni, M, Moller, K N, Sarr, M, and Johnson, A. 2008. Statistical modeling of global geogenic fluoride contamination in groundwaters. Environmental Science and Technology, Vol. 42, 3662–3668.
- Amini, M, Abbaspour, K C, Berg, M, Winkel, L, Hug, S J, Hoehn, E, Yang, H, and Johnson, A. 2008. Statistical modeling of global geogenic arsenic contamination in groundwater. Environmental Science and Technology, Vol. 42, 3669–3675.
Salinity
Salinity is an important groundwater quality issue in many parts of Africa, and can have important consequences for human health and agricultural productivity. Groundwater salinity can be driven by both natural and anthropogenic processes. Processes such as sea-level rise and intense evaporation (common under tropical climates) can lead to naturally high salinity in groundwater, while over-abstraction, irrigation and waste disposal can cause groundwater salinity or make natural salinity issues worse.
- IGRAC have compiled a global map of groundwater salinity by extrapolating documented cases into larger areas of high probability of saline occurrence.
Nitrate
Nitrogen occurs naturally in the environment and is essential for plant growth, but if it is present at high concentrations in groundwater or surface waters it can have a negative impact on both the environment and human health. Nitrogen-based fertilisers - both inorganic and organic (eg animal waste) are often applied to agricultural land in order to increase crop yields. Leaching from agricultural land can lead to high concentrations of nitrogen in groundwater.
- A British Geological Survey nitrate fact sheet gives an overview of nitrate in groundwater.
- IGRAC have carried out a global assessment of nitrate contamination, working towards global scale maps of nitrate in groundwater.
Urban pollution
Urban and peri-urban areas are expanding in many parts of Africa, particularly across sub-Saharan Africa. Groundwater is often a very important source of improved drinking water in urban and peri-urban environments, but high population densities put pressure on urban groundwater resources, not only in terms of quantity but of water quality.
Groundwater quality can be influenced by a large number of contaminants in the urban environment, from microbiological pathogens and heavy metals to macronutrients, herbicides and pesticides.
Some of the main sources of urban pollution include:
- pit latrines, which are often located close to abstraction points, particularly in densely populated peri-urban or unplanned urban settlements
- sewer leakage and sewage effluent
- uncontrolled disposal of household and industrial waste
- peri-urban agriculture, which includes pesticides/fertilisers and livestock waste
- storm water runoff
- vehicle emissions, power stations and mine waste
Urban groundwater issues in Africa are receiving increasing research attention in recent years, with more and more studies of both large and small cities and towns, and increasing detail in the chemical, microbiological and other groundwater quality parameters being studied.
Some overview studies of urban groundwater quality in Africa are:
Lapworth, DJ., Nkhuwa, DC.W., Okotto-Okotto, J. et al. 2017. Urban groundwater quality in sub-Saharan Africa: current status and implications for water security and public health. Hydrogeology Journal 25, 1093–1116
- Sorensen, JPR, Chibesa, M, Pedley et al. 2015. Emerging contaminants in urban groundwater sources in Africa. Water Research, 72, 51-63.
Africa Groundwater Atlas >> Resource pages >> Groundwater Quality