The influence of geology on the quality of groundwater for domestic use: a Kenyan review

Geology and hydrogeology of the Nyanzian Craton

The Archaean Nyanzian Craton, comprising of the Nyanzian and Kavirondian Systems are the oldest rocks in the country found in the western region and extend onto northern Tanzania and south–east Uganda forming part of the Tanzania Craton. The Nyanzian System is predominantly felsic volcanics and has less appearance of lavas and sediments (banded iron formations and chert) while the Kavirondian, which lies unconformably over the Nyazian is sedimentary dominant (rudites, arenites, and argillites) [19], 46], 47]. The dominant rocks in the region include granites, syenites, basalts, dacites, andesites, rhyolites, agglomerates and tuffs, chert, banded iron formations (Nyanzian) and conglomerates, greywackes and grits, and sandstones (Kavirodian) [19], 47]. Aquifers are located in Pleistocene sediments of sand and gravel and fractured and weathered layers of volcanics and borehole depths have a mean of 90 m and an average yield of 10 m³/h [13], 16].

Geology and hydrogeology of the Proterozoic Bukoban system (Kisii Series)

These rocks unconformably overly the Nyanzian System and cover the Kisii and Nyamira Counties in Western Kenya. The group is composed of andesitic basalts overlain by lapilli tuffs and lahar and sediments composed of siltites, conglomerates, chert, cinerite, and rhyolitic ignimbrite [19], 47]. There are no studies available on public domains characterising aquifer characteristics in the Kisii group.

Geology and hydrogeology of the Proterozoic Mozambique Mobile Belt

This region is found east of the Kenyan Rift Valley and covers most of the north–south of the central region of Kenya [19], 48]. Nyamai et al. [48] categorised the Kenyan Segment of the MMB into four segments which include the eastern segment, the southwestern segment, the northwestern, and northeastern according to where they appear in Kenya. These regions comprise various high-grade meta-sedimentary and meta-igneous rocks with a predominantly north–south structural trend covering the north-eastern to south-eastern region of Kenya and overlain by younger Tertiary volcanic rocks and recent sandy and loamy soils in some areas [49]. Dominant rocks include metasediments such as gneisses, schists, quartzites, migmatites, marble, granulites, and amphibolites as well as intrusives and meta-intrusives such as diorites, gabbros, and anorthosites [48].

Due to rock compactness and lack of primary porosity, aquifers in the metamorphic regions of Kenya have the least groundwater potential and are only localised in weathered and fractured zones within or in the boundaries of the rocks (secondary porosity) or in alluvial deposits along existing and old buried drainage channels [45], 50], 51]. Aquifer yield, static water level, and depth to water table vary within rock type, however, a general borehole yield of 4.5 m³/h and borehole depth of 55 m [45]. Due to the low productivity, low yield and seasonal boreholes, some of which dry up after some time, are common in regions such as Makueni, Machakos, and Taita-Taveta Counties [48], 51], 52].

Geology and hydrogeology of the Palaeozoic and Mesozoic sediments of northern and the coastal regions

These sediments are mostly found in the north-eastern and south-eastern regions of Kenya. They have been attributed to an intra-cratonic basin associated with the Gondwana land breakup during the Palaeozoic period [19]. Dominant sedimentary rocks include sandstones, grits, shales, limestones, conglomerates, and quartzites which are fluvio-deltaic and aeolian origin [19]. Shallow to deep marine environments in the Mesozoic favoured the deposition of limestones and shales.

Sedimentary aquifers make the largest aquifer system in the country by size, extending from the northeast region (Marsabit and Moyale) to the coastal region (Lamu) with an estimated maximum stretch of 740 km in length and 250 km in width [45]. In the northern region, the aquifer is relatively thin and shallow with reported thickness between 2 and 15 m and well depths of 6 m composed mainly of limestone overlaying sandy beds and silts and underlain by clay. Well yields are highly variable with most of the pump test producing a yield of 2 m³/h and a few 5 m³/h. Local direct recharge by rainfall feeds these aquifers which are drained by shallow wells by mostly pastoralists in the region.

The coastal region is covered by three major aquifers Msambweni, Tiwi and Sabaki which share a similar geology. These aquifers have a maximum stretch of about 80 km wide and reach up to a similar distance far inland from the coastline. The aquifer is composed mainly of sands intercalated with clays, coral, and limestone with a thickness range of 16–100 m and storativity of 20.1–92 Mm³ where most of them (above 65 % of the aquifer) are located above sea level (0–25 m asl) reducing the susceptibility of mixing with salt water [45], 53]. Groundwater heads from shallow wells and boreholes have been shown to vary between −3 and 30 m above sea level and increase inland from the sea level [53].

Geology and hydrogeology of tertiary volcanics and sediments of the Kenyan Rift Valley

The volcanic rocks are predominantly distributed along the Rift Valley region and the Kenyan highlands. The oldest of the rocks are found in the northern Kenya and South Nyanza regions and the youngest are towards the south. The rocks include basalts, trachytes, rhyolites, nephelinites, basanites, tuffs, basanites and ignimbrites [19]. In some areas of the Rift Valley, especially in toughs and volcanic succession bases, lacustrine and fluviatile Tertiary sediments are deposited.

The Rift Valley is a Caenozoic rift system onstage of separating the Somali subplate from the rest of the African plate. The rift runs in an N–S trend from Turkana in the North through to Magadi in the South and has varying volcanic and igneous suites with periodic lacustrine sedimentation in the lake basins on its floor. Aquifers are found in the fractured and weathered zone in rocks, lacustrine and other sediments intercalated between rocks while recharge is along the escarpments [19].

Several large aquifers in the rift include the Turkana aquifer in the northernmost part which extends for about 220 and 135 km in the N–S and E–W directions respectively and has a maximum transmissivity of 404 m²/day [45]. In the central rift, the Bogoria-Baringo aquifer stretches in a predominantly N–S trend of about 200 km and varies widely in the E–W direction with a transmissivity range of 100–1,600 m²/day [45]. Adjacent south, the Nakuru aquifer stretches around Lake Nakuru at about 100 km and stretches further south towards Lake Elementaita with a transmissivity range between 50 and 100 m²/day [45]. At the southern end of the Kenyan Rift Valley is the Magadi aquifer. the aquifer stretches from the south of Lake Naivasha in the north to the south of Lake Magadi in the south. The larger part of the aquifer has a width of about 80 km aquifer transmissivity ranges between 400 and 1,000 m²/day [45].

Drinking water quality in the Nyanzian Craton

The physicochemical characteristics of drinking water sources in the Nyanzian Craton are presented in Table 1. F⁻ concentrations in Kisumu County ranged between 0.3 and 11 mg/L with an average of 4.1 mg/L, where 50–81 % of boreholes and 30 % of shallow wells had higher values than the WHO recommended values [4], 17].

Groundwater facies characterising using Gibbs plot in the Kisumu region showed highly mineralised saline waters (Na⁺–Cl^‒ type) in the Awasi town [4], indicating high salinity in drinking water. In addition to the discussed geogenic groundwater quality issues, industrial contamination of surface water has been reported, where raw industrial effluent and municipal and agricultural wastewater have been reported to cause the death of aquatic life in Lake Victoria [15].

Only half of the population of Kisumu City has a piped water supply and even less (8 %) have proper sewerage [13]. Shallow groundwater abstraction in informal settlements in Kisumu City puts the local population at health risk due to the mixing of shallow groundwater with faecal matter from pit latrines, soak pits and septic tanks [2], 13]. Despite deeper boreholes showing safer drinking water in the area, this route to safe drinking water isn’t explored as these deep boreholes are not functional [2]. A comparative study on nitrate concentrations in shallow and deep wells (less than 10 m and more than 15 m, respectively) in Kano plan and Kisumu City showed higher NO₃ ⁻ (ranging between <0.04–90.6 mg/L) and NO₂ ⁻ (ranging between <0.04–3.2 mg/L) values than the WHO recommended values of 50 mg/L and 0.2 mg/L, respectively, in 63–75 % of boreholes and shallow wells in the region [4]. The study showed water sources (especially shallow wells) in highly populated sums to have higher NO₃ ⁻ values than less populated regions of the area while farm manure and fertilizer were associated with the elevated NO₃ ⁻ in deep boreholes in some parts of Kano and planned estates in Kisumu. Additionally [17], reported Thermal Tolerant Coliform (TTC) higher than the WHO recommended value (0 TTC/100 mL) in 95 % (n=22) of shallow groundwater sources in Kisumu City indicating contamination of shallow groundwater by faecal coliform.

Turbidity values in the Kisumu area range between 0 and 456 NTU [17] and these values higher than the recommended limit are noticed in boreholes, shallow wells and springs, with higher values noticed during the rainy season. The high turbidity was associated with geogenic sources including suspended soil and dissolved iron from laterites, as well as anthropogenic activities such as farming fields [17].

Drinking water quality in the Kisii Group volcanic and sedimentary aquifers

There are no groundwater geochemistry studies from the Kisii volcanic and sedimentary group region. However, several studies have highlighted the influence anthropogenic effects of water in the area and are highlighted here. In Kisii town, 95 % (n=41) of analysed spring water and 100 % (n=34) of shallow wells had faecal coliform which was attributed to contamination from pit latrines and septic tanks [54]. The contamination was also attributed to the high presence (50 %) of unprotected wells, which were categorised as high to very high risk of the frequency of sanitary hazards [54]. In the Manga region of Nyamira county, the water quality index showed good to excellent status (21.32–29.66) in the water, from three springs, which was deemed fit for domestic, industrial and agricultural use [55]. Other anthropogenic activities in Nyamira County such as sand harvesting along rivers, household wastewater and raw sewage disposal into the rivers as well as agricultural activities in Masaba North sub-county made the water turbid, murky and polluted rendering it undesirable and unhealthy to the local population [56].

Drinking water quality in the metamorphic Mozambique Mobile Belt

Most of the groundwater quality studies in the MMB are conducted in the eastern segment of the metamorphic rocks between Machakos, Makueni, and Kitui Counties with a Ca-Mg-HCO₃ water type [48]. There are several groundwater quality issues reported in areas covered by these metamorphic rocks such as F⁻, salinity, and iron.

Varying F⁻ concentrations have between reported in shallow wells and boreholes (0.3–8.2 mg/L) and a spring in Makueni, Machakos, and Kitui Counties [20], [50], [51], [52] as shown in Table 2. Concentrations higher than the WHO [57] and KEBS [58] recommended value of 1.5 mg/L in drinking water account for up to 50 % of analysed boreholes in these areas [52]. The high F⁻ concentrations in groundwater in these regions were reported as early as the 1980s [24], however, early studies, such as that of JICA [59], have been observed to categorise water sources with F higher than the recommended value of 1.5 mg/L as safe for human consumption, indicating that locals were allowed to use high F⁻ drinking water which caused health implications especially in Counties like Kitui County with groundwater dependence is as high as 90 % [60]. However, despite the limited number of studies, the metamorphic aquifers further south in Taita-Taveta have reportedly acceptable F⁻ concentrations of 0.28–1.24 mg/L [61].

The high F⁻ in groundwater in these metamorphic regions is reflected in its high values in food crops grown in the area. These include 288–700 mg/kg in vegetables (kale and cowpeas leaves) and 29–71.2 mg/kg in maize and legumes (cowpeas and green grams) [22].

Salinity is the concentration of inorganic salts, mostly Na, Ca, Mg, K, Cl⁻, SO₄ ⁻, and HCO₃ ⁻, in water, and can be expressed as the concentration of these parameters, their sum (cation + anion) or represented by physical parameters such as electrical conductance (due to dissolved salts), TDS, hardness, and alkalinity [11], 62], 63]. High salinity is a common issue in groundwater in crystalline basement aquifers [46]. In eastern Kenya, groundwater in metamorphic aquifers has been reported to have saline water of varying composition. In Makueni, Kitui and Machakos Counties, salinity and conductivity values ranging between 336 and 4,424 mg/L and 184–9,520 μS/cm, respectively were reported (as shown in Table 1), where, 50–100 % of the water sources have either higher conductivity and TDS than recommended values or poor-unacceptable salinity values [52], [64], [65], [66]. The other salinity-indicator parameters are also presented in Table 2. In Taita-Taveta, groundwater SO₄ ⁻ was reported as high as 1,299 mg/L in the Kasigau area [61] which is higher than the recommended value of 450 indicating high saline groundwater.

High salinity in crystalline aquifers found in arid to semi-arid regions such as eastern Kenya is contributed by the hot and dry weather causing evaporative concentration of salts in soils and shallow water, as well as long-term rock-water interaction causing mineral dissolution in deep aquifers [52], 67]. The high salinity in these regions has been linked to undesirable taste and gastrointestinal complications, which has resulted in the abandonment of some boreholes [52]. Other health implications such as high blood pressure, diarrhoea, and skin diseases have been shown to result from drinking high saline water [63], [68], [69], [70] need to be investigated in these high saline regions of Kenya. The lack of such research is evident by a report which showed that a significant number (61 %) of Kenyans living in rural regions have not been screened for high blood pressure [71]. In addition, research is needed to map groundwater salinity distribution in other regions known with salinity issues such as Taita-Taveta and parts of Nairobi and north-eastern Counties that draw water from metamorphic aquifers.

In the south-eastern Kenya region, iron concentrations ranging between 0.01 and 7.6 mg/L were reported in Makueni and Kitui Counties [51], 52], 60], 72] as shown in Table 1. this shows that some groundwater sources in the region have iron concentrations higher than the WHO and KEBS [57], 58] recommended value of 2 mg/L for drinking water. The only health implication reported from high Fe in drinking water was a ‘metallic’ undesirable taste of drinking water reported in Kitui County [60]. However, stains in clothes washed with high Fe water were also reported in Makueni County [51], 72]. There is a need for more studies on the health implications of high Fe drinking water use in the other regions covered by these metamorphic rocks, as high concentration in drinking water has been linked to cases of gastrointestinal upset, suppressed zinc and calcium absorption and constipation [73].

There is only one study [52] that reports the concentrations of potentially harmful trace metals (such as Cr, Co, Ni, As, Se, Cd and Pb) in groundwater in the metamorphic regions of Kenya. The study reported the values of these metals to be below the recommended values in drinking water in Makueni County. There are, therefore, more studies needed to know the concentrations of these metals in other areas of the metamorphic region due to their potential deleterious health effects even at very low concentrations [57]. Besides physicochemical parameters, bacterial contaminants such as E. coli have been identified in shallow wells dug close to pit latrines and septic tanks (as close as 5–7 m) in Kitui town [66], as well as in piped water from streams and springs in Kasigau hills of Taita-Taveta [61].

Drinking water quality in the volcanic rocks associated with the Rift Valley

The physicochemical characteristics of drinking water sources in the aquifers associated with the Rift Valley are presented in Table 3. The Kenyan Rift Valley, with a Na-HCO3 water-type, has been identified as a high-F⁻ province for quite some time [21], 24], 40], [74], [75], [76] both in surface and groundwater. In groundwater, F⁻ values ranging between 0.15 and 5.87 mg/L [77], 78] have been reported in the northern section of the Rift Valley around Turkana. The high F⁻ in the Turkana area was associated with the dissolution of the high-F⁻ minerals [77]. In the central region covering the Baringo-Naivasha area, F⁻ concentrations ranging between 0.01 and 75 mg/L have been reported both in shallow wells as well as boreholes [21], 40], 42], 76]. In the southern section covering Kajiado County, F⁻ concentrations between 0.8 and 15 mg/L have been reported in groundwater sources [79]. F⁻ concentrations in all the Kenyan Rift Valley lakes range between 2 and 140 mg/L [42], 80].

Since the volcanic rocks of the Rift Valley extend beyond the area, high F⁻ concentrations have been reported in groundwaters beyond the rift; such as 0.29–10.5 mg/L in Nairobi [81], 1.10–2.27 mg/L in Kiambu [82], and 0.21–9.30 mg/L in Machakos [83], 84].

Other potential groundwater contaminants reported in the Kenyan Rift Valley include heavy metals including Pb (0.8–2.64 mg/L), Zn (0.06–2.27 mg/L) and Mg (0–613 mg/L) as well as salts including Cl⁻ (5–15,670 mg/L), NO₃ ⁻ (0–371.85 mg/L) and SO₄ ⁻ (0.3–982.86 mg/L) which exceeded their recommended values in drinking water as shown in Table 2 [77], 78]. In Turkana, these high values of metals and salts were associated with oil drilling and hydraulic fracturing which contaminate nearby groundwater [78].

Drinking water quality in the sedimentary rocks of the coastal and northern Kenyan

Like other global coastal regions, groundwater contamination in the Kenyan coast is mainly associated with the vulnerability to seawater intrusion as well as aquifer mineral dissolution. Additionally, due to the rapid population growth in the Kenyan coastal region due to its industrialization, anthropogenic input to groundwater contamination cannot be ignored. In the northern drier parts of the coastal region, up to 50 % of the population relies on groundwater resources [85] and therefore monitoring its quality is important in the region.

The physicochemical characteristics of drinking water sources in the sedimentary aquifers of Kenya are presented in Table 4. Shallow groundwater (static water level of up to 8 m in some areas) makes aquifers on the Kenyan coast susceptible to surface contamination [53]. In the Mombasa area, the average concentrations of EC (993–10,585 mg/L) and TDS (438–5,281 mg/L) in boreholes (n=15) were higher than the WHO-recommended values (750 and 500 mg/L respectively) in 94 % of the sampled water sources by [53]. However, these values were slightly lower in Kwale County, south of Mombasa (EC=85.3–6,060 mg/L, TDS=90–907) [86], 87]. Sodium concentrations (average 254 g/L) in Mombasa were higher than the WHO-recommended value of 200 mg/L in 50 % of the samples [53]. Chloride concentrations (average of 161 mg/L) in Mombasa exceeded the WHO recommended value of 200 mg/L in 75 % of the water sources during the dry season where the maximum value of 369 mg/L was recorded. High Cl⁻ values (range between 30 and 1,635 mg/L) are also seen in Kwale County where 43 % (n=14) of the boreholes exceeded the recommended values [87]. The high EC, TDS Na and Cl⁻ concentrations in the groundwater indicate a salinity issue in the area, especially during the dry seasons. Temitope [53] reported a moderate vulnerability of the Mombasa aquifer to seawater intrusion.

This phenomenon is also observed in Kilifi County, located in the northern part of the Kenyan coast. Seawater intrusion has been reported in some areas which has led to the abandonment of some wells due to increased salinity of water over time [85]. Groundwater in the county was characterised by salinity which increased with depth and time, and cases of ‘iron taste’ from a borehole in Kituu [85], 88]. Higher EC values than recommended values were reported in 75 % (n=20) of both shallow wells and boreholes in Kilifi County by Makokha [85]. The study associated salt mining in the northern part of the county (Magarini) with the significantly high EC in groundwater in the area. Similarly, the study reported high TDS values, especially during the dry seasons, Cl⁻ and salinity in boreholes closer to the ocean and slightly hard to hard water. Most of the water sources had an E. coli count of more than 100 cfu/100 mL which is higher than the recommended value of 0 cfu/100 mL as was attributed to the disposal of untreated solid and liquid waste in the region [85].

Other potential contaminants reported in the Kenyan coastal region include lead in groundwater in Kwale County whose values ranged below the detection limit to 1.397 mg/L (mean value of 0.33 mg/L) where 62 % (n=37) of the sampled boreholes were above the WHO-recommended value of 0.01 mg/L [86].

The Nyanzian Craton

The geology of the Nyanzian Craton is composed of the oldest rocks in the country comprising both igneous and sedimentary rocks. The aquifers in the area are predominantly in the Pleistocene sediments (sand and gravel) and fractured and weathered volcanics with borehole depths of around 90 m. Shallow groundwater (less than 10 m) in Kisumu City, especially in highly populated settlements, and near farms in Kano Plain was associated with high NO₃ ⁻ (<0.04–90.6 mg/)and NO₂ ⁻ (<0.04–3.2 mg/L) which were higher than the WHO-recommended values, which was attributed to mixing of groundwater with sewage from put latrines, soak pits and septic tanks (in Kisumu) and farm manure and fertilizer in Kano Plain. The presence of high concentrations of Thermal Tolerant Coliform (TTC) in shallow waters in Kisumu indicates the presence of faecal coliform in the water. Deeper boreholes (>15 m) did not indicate sewerage or farm effluent contamination. High turbidity (up to 456 NTU) in both shallow and deep wells in Kisumu was associated with the dissolution of iron from laterites as well as farming effluent. High F⁻ (0.3–11 mg/L) was also reported in both boreholes and shallow wells in the Kisumu area. Highly mineralized saline water (Na⁺-Cl^‒ type), and conductivity (143–3,525 μs/cm), were also reported in Kisumu County [4], [13] which might affect drinking water palatability in the area.

From the geology of the area, high F⁻ can be associated with the presence of igneous rocks such as granites, basalts, and rhyolites, which have been shown to have high F⁻ concentrations in the Kenyan Rift Valley [42]. High turbidity can be attributed to high iron in the banded iron formations found in the area [19], 47]. Anthropogenic contamination is seen in the area by the presence of NO₃ ⁻ and NO₂ ⁻ in shallow wells in both urban settlement and farming areas indicating sewerage and farming effluent contamination. There is a need for a health study to determine the prevalence of health effects of high F⁻, NO₃ ⁻, and NO₂ ⁻, faecal matter reported in the area. Additionally, there is a lack of information on the concentration of potentially harmful trace metals such as Cr, Cu, As, Se, and Cd in the Nyazian Shield.

The Kisii Group

In the Kisii Group comprise basalts and tuffs as well as conglomerates, chert, and rhyolitic ignimbrites. However, there are no studies in the public domain reporting on aquifer characteristics in the Kisii and Nyamira Counties where these rocks cover. Shallow wells in Kisii town were categorized as high-risk health hazards due to the presence of faecal coliform contamination from pit latrines and septic tanks [54]. In Nyamira County, spring water showed a good-excellent water quality index [55], However, human activities including sand harvesting and disposal of untreated wastewater have been reported to pollute rivers in the County [56]. There is a lack of studies on groundwater quality analysing all the chemical elements in the Kisii Group that can potentially come from geogenic sources, which is wanted in the area. Additionally, the health effects of the faecal coliform contamination reported in shallow groundwater need to be established in the area.

The Mozambique Mobile Belt

The Mozambique Mobile Belt is dominated by various meta-sediments and meta-igneous rocks, such as gneisses, schists, and migmatites, and covers the north–south of the central region of Kenya [19], 48]. Aquifers are located in fractured, weathered and contact zones of these rocks with average borehole depths of 55 m [45]. Groundwater quality in the eastern segment of the belt has been extensively studied.

Among the commonly reported contaminants, F⁻ concentrations above recommended values have been reported in Makueni (0.6–8.2 mg/L), Kitui (0.30–2.47 mg/L), Machakos (0.21–9.3), while Taita Taveta County has concentrations within recommended limits (0.28–1.24 mg/L) as shown in Table 3. Fluoride concentrations range between 0 and 3.47 mg/kg in farm soils in Makueni County and were associated with the leaching of apatite, muscovite and biotite metamorphic rocks in the area [22]. Cases of dental fluorosis have been reported in Makueni and Machakos Counties indicating the health implications of the high F⁻ in the region [83], 89]. There is a need to establish a F⁻ hazard map in aquifers of the Mozambique Belt as well as a F⁻-related disease prevalence map to determine the most affected regions where defluoridation programs can be encouraged.

High salinity (336–4,424 mg/L) has been reported being a common issue in the Makueni, Machakos, Taita-Taveta and Kitui Counties (Table 3). This has been known to be a common issue in most basement aquifers due to the dissolution of the crystalline rocks [46]. The high salinity has caused undesirable water taste and gastrointestinal complications causing some boreholes to be abandoned [52]. There is, however, a need for further studies in the region on health implications such as high blood pressure, diarrhoea, and skin diseases that have been shown to result from drinking high-saline water [63], [68], [69], [70]. Desalination programs are also recommended in most public water systems in the region.

High iron concentrations (0.01–7.6 mg/L) than recommended values (Table 3) were reported in Makueni and Kitui Counties which caused a ‘metallic’ taste in drinking water [60]. The high iron can be attributed to the metamorphic rocks in the area. There is a need for further studies on the health effects of high iron in drinking water in the area. Potentially harmful trace metal concentrations (such as Cr, Co, Ni, As, Se, Cd and Pb) were lower than recommended values in Makueni County [52].

Paleozoic and Mesozoic sedimentary regions of Kenya

These are sedimentary rocks including sandstones, grits, shales and limestones found in the north–eastern and south–eastern regions of Kenya. Aquifers in these regions are the largest in Kenya [45] and occur in sands, corals and limestones. Concentrations of Sodium (average 254 g/L), chloride (average of 161 mg/L), EC (993–10,585 mg/L) and TDS (438–5,281 mg/L) higher than the recommended values in drinking water were reported in Mombasa, Kilifi and Kwale indicating high salinity in groundwater in the three counties, which had led to the abandonment of some wells in Kilifi County [85]. The high salinity in the coastal aquifers was linked to seawater intrusion and salt mining activities in Kilifi County [85]. Lead concentrations (up to 1.4 mg/L) above recommended limits were reported in groundwater in Kwale County but there was no indication whether the source was geogenic or anthropogenic. The presence of E. coli counts higher than recommended values in drinking water was reported in Kilifi County indicating anthropogenic contamination of shallow groundwater resources. There is a need for a health study to determine the health effects of the high salinity as well as E. coli presence in drinking water in the area. The extent of seawater intrusion also needs to be established in the Kenyan Coastal aquifers to know the affected aquifers and mitigate the issue. Alternative water sources such as piped water should be encouraged to reduce the stress on fresh water aquifers in the coastal region.

Tertiary volcanics and sediments

Tertiary volcanic rocks in Kenya, including basalts, trachytes, rhyolites, nephelinites, basanites and tuffs are associated with the formation of the Rift Valley, and they cover the Rift region, north–south in central Kenya and the areas next to the Rift Valley. Aquifers are found in fractured and weathered zones in rocks as well as lacustrine sediments in the Rift floor. Most studies on groundwater quality in the Rift Valley report high F⁻ concentrations in most of the areas covered by these volcanic rocks such as Turkana, Baringo, Nakuru, Nairobi, Kiambu, and Kajiado Counties (Table 3). These studies are similar to those in Ethiopia, Tanzania, and Uganda which report high F⁻ in the groundwaters of the Rift Valley [90], 91]. High F⁻ concentrations of up to 140 mg/L have similarly been reported in the Rift Valley lakes [42], 80]. The dissolution of F⁻ from the volcanic rocks through water-rock interaction and evaporative concentration has been attributed as the main processes contributing to the high F⁻ in aquifers in the Rift Valley aquifers [40], 42].

Food crops grown in these volcanic regions have also reported elevated F⁻ concentrations such as 7–53 mg/kg in vegetables (kale and pumpkin leaves) from Muranga, Meru, Kirinyaga and Kericho Counties, and 10–88 mg/kg from cowpeas from Kisii, Kericho and Nakuru Counties [92], 93]. Apart from F⁻, high concentrations of lead, zinc, magnesium, chlorides, nitrates and sulphates were also reported in groundwater in Turkana County [78]. Other potentially harmful contaminants in drinking water have not been reported in the region. Due to the extremely high F⁻ concentrations reported across the Kenyan Rift Valley and its environs, there is a need for establishing a F⁻ hazard map to know contaminated aquifers and food crops. Defluoridation programs should be established in the Rift Valley region to reduce the effects of the high F⁻. Due to the wide extent of the Tertiary volcanic aquifers, there is a need to establish their interactions and interconnections with other aquifers for possible contamination. This is especially true in the eastern region, with cases of dental fluorosis, where volcanic and metamorphic rocks overly each other [52].

Water quality management is an important aspect of every country to ensure the provision of safe, reliable, and adequate water to its citizens. This can be achieved through systematic data collection, processing, analysis and cataloguing of the results of water quality status which can be accessible for decision-making in all the industries using the different water resources in the country [8], 94]. Kenya is still lacking proper data management of the quality of its water resources mainly because of a lack of adequate and reliable data as well as poor handling, processing, achieving and distribution [12].

The Kenyan Ministry of Water and Irrigation created a drinking water quality surveillance programme in 1992. Challenges including inadequate equipment, funding allocation, and proper management have stalled their operations which are handled by several organizations such as (the Water Resources Management Authority) (WRMA) [12]. For example, the national water quality management team at the ministry was at 40 % capacity in a ministry report of 2016 [12]. In addition, the report also indicated that different institutions under the ministry do not have clear specifications on the roles shared amongst them, which might lead to neglecting some tasks.