Hydrogeology of Kenya

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 Africa Groundwater Atlas >>  Hydrogeology by country >> Hydrogeology of Kenya


Maxwell Barasa, Rural Focus Ltd, Kenya

Emily Crane, Kirsty Upton, Brighid Ó Dochartaigh, British Geological Survey, UK

Geographical Setting


Kenya ranges in elevation from sea level to over 5,500 m, and can be divided into a number of physiographic units, including the the coastal belt and plains; plateaux; plains; highlands (western and eastern); and the Kenya Rift Valley.

Political Map of Kenya (For more information on the datasets used in the map see the geography resources section)

Estimated Population in 2013* 44353691
Rural Population (% of total)* 75.2%
Total Surface Area* 569140 sq km
Agricultural Land (% of total area)* 48.2%
Capital City Nairobi
Region Eastern Africa
Border Countries Somalia, Ethiopia, South Sudan, Uganda, Tanzania
Annual Freshwater Withdrawal (2013)* 2735 Million cubic metres
Annual Freshwater Withdrawal for Agriculture* 79.16%
Annual Freshwater Withdrawal for Domestic Use* 17.18%
Annual Freshwater Withdrawal for Industry* 3.66%
Rural Population with Access to Improved Water Source* 55.1%
Urban Population with Access to Improved Water Source* 82.3%

* Source: World Bank


Kenya's climate varies from almost equatorial to high alpine.

Rainfall time-series and graphs of monthly average rainfall and temperature for each individual climate zone can be found on the Kenya Climate Page.

Average monthly precipitation for Kenya showing minimum and maximum (light blue), 25th and 75th percentile (blue), and median (dark blue) rainfall Average monthly temperature for Kenya showing minimum and maximum (orange), 25th and 75th percentile (red), and median (black) temperature Quarterly precipitation over the period 1950-2012 Monthly precipitation (blue) over the period 2000-2012 compared with the long term monthly average (red)

For further detail on the climate datasets used see the climate resources section.

Surface water

Kenya's main rivers originate in the central highlands or in the southern foothills of the Ethiopian highlands. The Rift Valley is a dominant control on surface water flows. West of the Rift Valley, surface water flows towards Lake Victoria and into the Nile Basin; east of the Rift Valley, surface water flows southeast to the Indian Ocean. For the water resource management purposes, five main catchments are identified: Lake Victoria basin, Rift Valley basin, Athi river basin, Tana river basin and Ewaso Ngiro river basin (Pavelic et al. 2012). These large basins are in turn subdivided into 52 main basins and sub-basins (United Nations 1989).
Surface Water Map of Kenya (For more information on the datasets used in the map see the surface water resources section)


Soil Map of Kenya (For the map legend and more information on the datasets used in the map see the soil resources section)

Land cover

Kenya includes a number of distinct ecological zones, including Alpine grasslands at high altitudes; humid to dry sub-humid zones; semiarid zones; and arid zones.
Land Cover Map of Kenya (For the map legend and more information on the datasets used in the map see the land cover resources section)


This section provides a summary of the geology of Kenya. More detail can be found in the references listed at the bottom of this page. Many of these references can be accessed through the Africa Groundwater Literature Archive.

The geology map on this page shows a simplified version of the geology at a national scale (see the Geology resources page for more details). The map is available to download as a shapefile (.shp) for use in GIS packages.

Kenya Geology.png

Geological Environments
Key Formations Period Lithology Structure
Sedimentary - largely unconsolidated
Baratamu Formation (Miocene-Eocene); Marafa Formation and Magarini Sands (Pliocene); Kilindini Formation (Pleistocene); and Recent deposits Tertiary-Quaternary Sedimentary deposits are common in various parts of Kenya, usually occuring at the base of, or intercalating with, volcanic successions, or deposited in tectonic troughs. The repeated faulting of the Rift Valley floor and the numerous volcanic eruptions created many short-lived basins with internal drainage in which lacustrine and fluviatile sediments accumulated. Sediment types include soils; alluvial and coastal beach sands and dune sands, evaporates, fossil coral reef and lagoonal formations and coastal sandstones; and alluvial and lacustrine sediments in the Rift Valley.

Most of these sediments are unfossiliferous, but a few are of interest as they contain deposits that bear artefacts and interesting fossils that have been studied extensively. The more important sediments of middle Pleistocene are the Olorgesaillie lakebeds, a lacustrine series with much diatomite, mammalian fossils and artefacts. This is also comparable to the Kariandusi sediments near Gilgil and the Kanjera Beds in the Kavirondo Gulf off Lake Victoria. Olorgesaillie beds and Kariandusi sediments occur in the Rift Valley. Some early Tertiary formations do not crop out at the ground surface.

Igneous Volcanic
Tertiary-Quaternary Volcanic rocks cover the central parts of the country from south to north, occurring in the floor of the Rift Valley and on the peneplains west and east of the valley.

The oldest are of Lower Miocene age and comprise the eroded lavas and pyroclastic piles of South Nyanza. Late in Miocene times, Kapiti and Yatta phonolites were erupted and flowed to great lengths. Further eruptions accompanied by faulting persisted and also gave rise to the Rift Valley and the volcanic piles of Mounts Kenya, Elgon and Kilimanjaro.

Quaternary volcanism was mostly within the Rift Valley and has given rise to the craters and cinder cones that are found in the floor of the valley, e.g. Longonot, Menengai and Suswa.

Sedimentary – Mesozoic-Palaeozoic
Mtombku Formation (Jurassic-Cretaceous); Kambe Limestone & Mazeras Formation (Jurassic); Mariakani Sandstone (Triassic); Maji-ya-Chumvi (Permian-Triassic) and Taru Grits (Permian) Mesozoic-Palaeozoic Palaeozoic and Mesozoic formations in Kenya are found near the coast and in the northeast.

The oldest of these rocks include the Taru, Maji-ya-Chumvi, Mariakani and Mazeras formations, which are dominantly sandstones, shales and siltstones, and form the Duruma series - equivalent to the Karroo system in southern Africa. They extend for about 100 km from Taru to Mazeras, west of Mombasa.

Younger rocks occur in two separate areas, in the northeast of Kenya and along the coastal belt. The sratigraphy and fossils in the two areas are very distinct and it is likely that the sedimentary basins in the two areas were connected. Revision mapping in the area has come up with interesting lithological units that have revised lithological names. They include limestones as well as sandstones, siltstones and shales, including the Kambe Limestone and Mtombku Formation.

The rocks of the Duruma series between Taru and Mazeras dip very gently towards the ocean and are heavily faulted in places.
Bukoban system and Mozambique Belt Proterozoic The Kisii series of the Bukoban system comprises metamorphosed volcanic rocks with metasedimentary rocks.

The Mozambique belt is a structural unit within which a wide variety of metasedimentary and meta-igneous rocks are found, with a broad concordance of structural style and metamorphic history. The degree of deformation is intense in most of the rocks, and they are of high metamorphic grade. They were referred to in earlier literature as basement system rocks, due to the high degree of metamorphism and deformation. Recent work on the Mozambique Belt has shown that rocks can be sub-divided into groups of contrasting lithology, structure and composition of igneous rocks content. Rock types include quartzites, biotite/hornblende gneisses, schist, granitoid gneisses, amphibolites and migmatites, and there are intrusions of syntectonic granites. These groups are being studied in greater detail in order to come up with proper chronostratigraphic terminology. Within the Mozambique Belt, basic igneous complexes range in size from bosses to small dykes. They occur both east and west of the Rift Valley. Some of the older basic intrusions have undergone deformation and metamorphism to give orthoamphibolites and charnockitic gneisses. Basic and granitic intrusions are known in the Mozambique Belt. The majority of Mozambique rocks have been placed in upper Precambrian (Proterozoic).

The most characteristic feature of the Mozambique Belt is its structural trend, which is more or less north-south across the entire belt. Variations of the northerly trend are minor and when observed can be explained and are localised.
Kavirondian and Nyanzian Archaean The Nyanzian and Kavirondian systems forming the Nyanza Craton are the oldest rocks in the country, with ages over 2,500 million years.

The Nyanzian system is mainly composed of lavas and pyroclastics with minor sediments (including shales and cherts) and banded ironstones.

The Kavirondian, which rests uncomfortably on the Nyanzian, consists of grits, sandstones, mudstones, greywackes and conglomerates.

Numerous granitic bosses and batholiths have intruded the Nyanzian and Kavirondian. There are more Kavirondian intrusions, but pre-Kavirondian intrusions are also widespread, and the two systems are discernible.

Both the Nyanzian and Kavirondian systems are isoclinally folded about axes that have an east-westerly trend. Kavirondian, is only slightly younger than Nyanzian but folding in the two systems has similar orientation.


This section provides a summary of the hydrogeology of the main aquifers in Kenya. More information is available in the references listed at the bottom of this page. Many of these references can be accessed through the Africa Groundwater Literature Archive.

The hydrogeology map on this page shows a simplified version of the type and productivity of the main aquifers at a national scale (see the Aquifer properties resource page for more details). The map is available to download as a shapefile (.shp) for use in GIS packages.

Kenya Hydrogeology.png Hydrogeology Key.png


The Water Resources Management Authority (WRMA) classifies Kenya's aquifers as follows:

Class Description Examples
Strategic aquifer Aquifer used to supply significant amounts/ proportions of water in a given area and for which there are no available alternative resources, or where such resources would take time and money to develop; significant transboundary aquifers Sabaki, Tiwi, Nairobi, Central Merti, Nakuru, Kabatini, Lake Naivasha Lamu Island
Major aquifer High-yield aquifer systems with good quality water Daua and Elgon volcanics Minor aquifer Moderate-yield aquifer systems with variable water quality. Mandera Jurassics
Poor aquifer Low- to negligible-yield aquifer systems with moderate to poor water quality. Basement System
Special aquifer Aquifer systems designated as such by WRMA Isinya

The following summary classified Kenya's aquifers differently, by their geological environment, which controls the way in which groundwater occurs and behaves in the different aquifers.

Sedimentary - Unconsolidated and Semiconsolidated; Intergranular Flow

Named Aquifers General Description Water quantity issues Water quality issues Recharge

Lotikipi and Lodwar aquifers Alluvial sands and sediments, which range up to 80 m deep. They can have high groundwater potential where dominated by coarse grained sediments (sand and gravel), but elsewhere, groundwater potential is typically limited. Groundwater in the Lotikipi aquifer is very saline, with conductivity values exceeding 8000 uS/cm. Recharge occurs both by direct rainfall infiltration and, to the Lodwar aquifer, by leakage from the River Turkwel.
Tiwi aquifer Occurs in the Kwale area. The lithology is alluvial sand and clay. High yields can be obtained. Boreholes are typically 40 – 80 m deep. Typically good quality. Vulnerable to saline intrusion.
Gongoni/Msambweni Aquifer The Gongoni/Msambweni Aquifer occurs in the Kwale area. High yields can be obtained. Boreholes are typically 40 – 100 m deep. Generally good quality, apart from high iron concentrations. Recharge occurs by direct rainfall infiltration and also by leakage from the River Mkurumudzi.
Baricho Aquifer The Baricho Aquifer occurs in the Malindi area and comprises alluvial sand and gravel, from which good yields can be obtained. Boreholes are typically drilled to 25 – 60 m depth. Generally good quality, sometimes elevated total dissolved solids (TDS) Recharge occurs by direct rainfall infiltration and also by leakage from the River Galena.
Merti Aquifer The Merti Aquifer occurs in Wajir County and comprises semi-consolidated clays, sands, sandstones and limestones (Mumma et al. 2011). Groundwater is often confined and found at fairly uniform depths of between 110 and 180 m below ground level. Successful boreholes tap the more permeable zone of the Merti Formation commonly between 105 m to 150 m bgl (GIBB Africa Ltd 2004). The actual thickness of the Merti Aquifer is not known, because few boreholes fully penetrate the aquifer (Oord et al. 2014). Locally subject to over-exploitation (Mumma et al. 2011) Saline water has been observed in the Merti aquifer and is also believed to underlie the fresh water layer. Water quality in the Dadaab refugee camps has deteriorated over time, mainly due to increasing salinity. In Habaswein there is evidence of some salinisation as a result of long term abstraction (Mumma et al. 2011, Oord et al. 2014).

Key references for these aquifers are Acacia Water, GIBB Africa Ltd (2004), Mumma et al. (2011) and Oord et al. (2014) (see Reference section, below).

Igneous Volcanic

Named Aquifers General Description Water quantity issues Water quality issues Recharge
General volcanic aquifers The volcanic rocks in Kenya vary from a few metres to several hundred metres thick. Groundwater flow and storage occur in fractures and weathered zones, often along the sub-horizontal boundaries between successive lava flows, which at one time were land surfaces. Boreholes in the volcanic aquifers are up to 125 m depth, and may encounter more than five discrete aquifer layers. These aquifer layers are often confined. Yields, depth to aquifers and rest water levels vary significantly. A specific capacity value of 0.2 m³/hour/m is quoted (Pavelic et al. 2012, Ministry of Water Development 1992). An average yield of 7.5 to 7.6 m³/hour is quoted for boreholes in volcanic rocks (Pavelic et al. 2012, United Nations 1989), with a large drawdown of 37 m (Pavelic et al. 2012). A hydraulic conductivity value of 0.0144 m/d is quoted. Groundwater typically has low total dissolved solids and high bicarbonate. The volcanic deposits of the East African Rift System are rich in fluoride which leads to high groundwater fluoride concentrations. For example, concentrations over 10 mg/L were found in the Nairobi area (Coetsiers et al. 2008).
Nairobi Aquifer This aquifer occurs in the Nairobi area and comprises layered volcanics interbedded with old land surface and intervolcanic sediments. Boreholes are typically drilled to 250 - 400 m depth. Overabstraction causing lowered water levels. Generally good quality. Recharge from Ngong Hills.
Kabatini aquifer The Kabatini aquifer occurs within the volcanic rocks of the Nakuru area. Boreholes are typically drilled to about 150 m depth. Elevated fluoride concentrations.
Gongoni and Baricho aquifers

A key reference for these aquifers is Coetsiers et al. (2008).

Consolidated Sedimentary - Intergranular & Fracture Flow

Named Aquifers General Description Water quantity issues Water quality issues Recharge
Mazeras Formation, Karoo General Description of aquifer Water quantity issues Water quality issues Recharge


Named Aquifers General Description Water quantity issues Water quality issues Recharge
Name of aquifer An average yield of 4.4 m³/hour is quoted for boreholes in Precambrian basement aquifers (United Nations 1989).

Water quantity issues Water quality issues Recharge

Groundwater Status

Groundwater quantity

The groundwater potential of Kenya is estimated to be 619 million m³ (Pavelic et al. 2012). The total groundwater abstraction rate in Kenya in 2012 was estimated at 7.21 million m³/year. Total safe abstraction rate in Kenya is estimated to be 193 million m³/year (Ministry of Water Development 1992, Pavelic et al. 2012).

Groundwater quality

Some aquifers, mostly with recharge from fresh water rivers, are excellent groundwater sources e.g. the Lodwar Aquifer recharged by the River Turkwel; the Merti Aquifer recharged by the River Ewaso; the Gongoni Aquifer recharged by the Mkurumudzi River and the Baricho Aquifer recharged by the River Galena.

Many aquifers have groundwater quality issues. For example, the Nairobi aquifer has high fluoride concentrations, which mostly exceed WHO standards, especially towards the Embakasi area.

The Lotikipi Aquifer is very saline with conductivity exceeding 8000 µS/cm.

Surface water-groundwater interaction

Various contamination problems arise due to the hydraulic continuity between surface water and shallow groundwater systems in Kenya, e.g.:

  • Poor sewerage and drainage systems are major contributors to groundwater contamination. This is an increasing problem in Nairobi and its environs.
  • Open cast mining of stones pose a threat to groundwater as a result of contaminated water infiltrating into the ground.
  • The Kiserian reservoir has suffered contamination problems due to inadequate sewage systems in nearby towns; this contaminated water may find its way into groundwater. Equally, groundwater may be becoming directly contaminated as a result of reliance on pit latrines and soakaway pits.
  • River pollution by industrial wastes and sewage pose a great risk for groundwater protection.

Groundwater use and management

Groundwater use

It is reported that although groundwater exploitation has considerable potential for boosting water supplies in Kenya, its use is limited by poor water quality, overexploitation, saline intrusion along the coastal areas, and inadequate knowledge of the occurrence of the resource (Mumma et al. 2011). Nevertheless, many areas of Kenya are reliant on groundwater sources for domestic, commercial and industrial needs, including the coastal zone which is almost entirely dependent on groundwater. Other areas include Mombasa and Malindi (which depend on the Baricho wellfield); Kwale (dependent on the Tiwi wellfield); and Wajir (dependent on the Merti aquifer); as well as Naivasha, Nakuru, Mandera, and Lodwar (Mumma et al. 2011).

Groundwater is used locally for mining, e.g. the Gongoni well field used for the Base Titanium mining company.

The Daadab refugee camp depends on groundwater abstracted from the Merti aquifer.

Groundwater management

Legislation and regulation

The principal policy framework for Kenya's water sector reform process is Sessional Paper No. 1 of 1999, National Policy on Water Resource Management, and Development (Mumma et al. 2011). The Water Act of 2002 creates the mechanisms for planning, including the establishment of the Water Resources Management Authority (WRMA). It regulates the ownership and control of water and makes provision for the conservation of surface and groundwater and the supply of services in relation to water and sewerage (Mumma et al. 2011). The Act provides that WRMA will formulate National Water Resources Management Strategy. In 2006, WRMA proposed a policy for the protection of groundwater (Mumma et al. 2011).

However, there are still few regulations in place that effectively control groundwater management, allocation, and protection. One of the obstacles to this is the effect of the common law on groundwater, which states that a private landowner effectively owns the resource and can abstract it and put it to his own use without having to take account of the wider social requirements (Mumma et al. 2011).

Key agencies

Some of the key agencies involved in groundwater management are listed below. Others can be seen in Mumma et al. (2011).

The Ministry of Water and Irrigation (MoWI) is responsible for the development of legislation, policy formulation, sector coordination and guidance, and monitoring and evaluation.

The Water Resources Management Authority (WRMA) is reponsible for, among other things, water resources planning, management and protection and monitoring; issuing water permits; water rights and enforcement of permit conditions; regulation and control of water use; and catchment and water quality management.

Catchment Area Advisory Committees (CAACs) are responsible for advising WRMA on water resources issues at catchment level.

Groundwater monitoring

Transboundary aquifers

Kenya shares several transboundary aquifers with neighbouring countries, defined by IWMI (2014) as:

  • AFS31 Coastal sedimentary basin 1 (Kenya/Tanzania) - Quaternary and consolidated sedimentary rocks
  • AFS32 Kilimanjero aquifer (Kenya/Tanzania) - Volcanic alluvium
  • AFNE1 Rift aquifer (Kenya/Tanzania/Uganda) - Volcanic
  • AFNE2 Merti aquifer (Kenya/Somalia) - Semi-consolidated sedimentary
  • AFNE3 Mount Elgon (Kenya/Uganda) - Volcanic
  • AFNE4 Dawa (Ethiopia/Kenya/Somalia) - Volcanic rocks, alluvials and Precambrian basement
  • AFNE5 Juba aquifer (Ethiopia/Kenya/Somalia) - Aquifers in Precambrian and intrusive rocks
  • AFNE7 Sudd basin (Ethiopia/Kenya/South Sudan/Sudan) - Precambrian and volcanic rocks with patches of alluvials/sedimentary

Source: IWMI. 2014. Transboundary Aquifer Mapping and Management in Africa. http://www.iwmi.cgiar.org/Publications/Other/PDF/transboundary_aquifer_mapping_and_management_in_africa.pdf

For further information about transboundary aquifers, please see the Transboundary aquifers resources page

Groundwater monitoring


The following references provide more information on the geology and hydrogeology of Kenya.

These, and others, can be accessed through the Africa Groundwater Literature Archive

Geology: key references

Hydrogeology: key references

Acacia Water. Hydrogeological Assessment of the Merti Aquifer, Kenya. Technical report no 1 of ARIGA. Assessing Risks of Investment in Groundwater Development in Sub-Saharan Africa. http://www.worldagroforestry.org/sites/default/files/TR1%20ARIGA-%20Hydrological%20Assessment%20of%20the%20Merti%20Aquifer%20Kenya.pdf

Adams B. 1986. Tiwi Aquifer Study, Final Report. Prepared on behalf of British Geological Survey for the Ministry of Water Development, Kenya, and British Technical Cooperation/

Carruthers RM. 1985. Report on Geophysical Studies Relating to the Coastal Aquifer of the Mombasa District, Kenya. Rep. Reg. Geophy. Research Group. British Geological Survey, No. RGRG 85/4. Keyworth, Nottingham http://nora.nerc.ac.uk/505659/1/WK_RG_85_4.pdf

Coetsiers M, Kilonzo F and Walraevens K. 2008. Hydrochemistry and source of high fluoride in groundwater of the Nairobi area, Kenya, Hydrological Sciences Journal, 53:6, 1230-1240, DOI: 10.1623/ hysj.53.6.1230

GIBB Africa Ltd. 2004. UNICEF Kenya Country Office - Study of the Merti Aquifer - Technical Report ISsue 2.0.

Mumma A, Lane M, Kairu E, Tuinhof A and Hirji R. 2011. Kenya: Groundwater Governance Case Study. Water Papers: Water Partnership Programme. http://www.groundwatergovernance.org/fileadmin/user_upload/groundwatergovernance/docs/Country_studies/GWGovernanceKenya.pdf

Ministry of Water Development. 1992. The Study on the National Water Master Plan. Prepared with the assistance of Japan International Cooperation Agency (JICA).

Oord A, Collenteur R and Tolk L. 2014. Hydrogeological Assessment of the Merti Aquifer, Kenya. Technical report no 1 of ARIGA. Assessing Risks of Investment in Groundwater Development in Sub-Saharan Africa. http://www.worldagroforestry.org/sites/default/files/TR1%20ARIGA-%20Hydrological%20Assessment%20of%20the%20Merti%20Aquifer%20Kenya.pdf

Pavelic P, Giordano M, Keraita B, Ramesh V and Rao T. 2012 . Groundwater availability and use in Sub-Saharan Africa: a review of 15 countries.. International Water Management Institute.

Sincat-Atkins/Groundwater Survey (Kenya) Ltd (JVSA/GSK). 1998. Second Mombasa & Coastal Water Supply Engineering and Rehabilitation Project - Tiwi Aquifer Development: Borehole Drilling and Associated Works; Borehole Completion Report. Volume I-III. Report for National Water Conservation & Pipeline Corporation, prepared by Joint Venture Sincat-Atkins in association with Groundwater Survey (K) Ltd. Nairobi, Kenya.

Sosi B, Cheboi E and Simiyu C. 2013. Nonlinear Correlation analysis between Surface Resistivity and Hydraulic Characteristics of the Kabatini Well Field, Upper Lake Nakuru Basin, Kenya Rift. IOSR Journal of Applied Geology and Geophysics (IOSR-JAGG), Volume 1, Issue 6 (Nov – Dec 2013), 35-45. http://iosrjournals.org/iosr-jagg/papers/vol1-issue6/E0163545.pdf

United Nations. 1989. Groundwater in Eastern, Central and Southern Africa: Kenya. United Nations Department of Technical Cooperation for Development.

Other sources of data and information

  • The Ministry of Mining – sells geological maps and geological reports carried out by the Geological Survey of Kenya: http://www.mining.go.ke/
  • The Water Resources Management Authority licences hydrogeological data (borehole logs, aquifer units and yields): http://www.wrma.or.ke/

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