Mr. Japhet Rugendo Kanoti

To enhance capacity through research, provide world class services in groundwater resource management and sustainable use of the sub-surface as a repository of waste and a source of water to the humanity and to provide and mainstream innovative scientific, technological and policy solutions for sustainable development of our changing earth.

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Kanoti, J, Olago D, Opiyo N, Nyamai C, Dulo SI, Taylor R.  2019.  Characterisation of geogenic controls on groundwater quality in a volcano-sedimentary aquifer in Kenya using graphical and statistical methods, 26 Sep 2019. 46th IAH Congress. , Malaga, Spain Abstractcontribution.pdf

Geogenic controls on groundwater quality are often dominant but remain inadequately characterized for many aquifer systems. The volcano-sedimentary aquifer of Kisumu (Kenya) is used widely to provide safe water to the informal settlements and acts as a strategic, supplementary supply to the city during interruptions in service from the main piped water supply network drawing from Lake Victoria. Little is known, however, of the geogenic controls on groundwater quality in the Kisumu aquifer. We characterize the origin and composition of solutes in groundwaters sampled from the Kisumu aquifer using a range of techniques. Classical graphical methods (i.e. Durov, Piper, Schoeller, Stiff and Ternary plots) were used as interpretative tools of the main hydrogeochemical processes whereas principal component analysis (PCA) and hierarchical cluster analysis (HCA) methods were used to assess hydrochemical variations and water types. An agglomeration schedule with five cluster solutions and between-groups linkage method of clustering using the squared Euclidian distance was employed. Variables were standardized to z-scores so that each variable contributed equally to the clusters. The study identifies three main groundwater geochemical signatures in the Kisumu study area: cation exchange (Ca-Na, Ca-Mg) between aqueous and solid phases, the chemistry of recharge water, and groundwater mixing. The concentration of major ions in groundwater varies with geology and also seasonally. The dominant water facies is Na-Ca-HCO3 type; other hydrochemical facies include Ca-Mg-HCO3 and Na-HCO3. Hydrochemical plots suggest that dissolution of carbonates and halite are the other major chemical processes, in addition to cation exchange, that control the groundwater chemistry in the Kisumu aquifer. Hierarchical cluster analysis of the main cations and anions discriminated satisfactorily the various water types in the study area.

Kanoti, JR, Olago D, Opiyo N, Nyamai C, Dindi E, Kuria Z.  2019.  Characterization of Major Ion Chemistry and Hydro-Geochemical Processes in Mt. Elgon Trans-Boundary Aquifer and Their Impacts on Public Health. Journal of Environment and Earth Science. 9(4):38-45. AbstractWebsite

There is a gradual paradox shift from the utilization of surface water to groundwater in both urban and rural Kenya. This is because surface water is both diminishing in quantity due to climate variability and deteriorating in quality due to high levels of anthropogenic contamination. In the quest to attain the Sustainable Development Goal number 6 that aim at ensuring access to safe water by all by 2030, the Government of Kenya is encouraging the development of groundwater resources whose potential is enormous though it has not been quantified. The Inter-governmental Authority on Development (IGAD) supported this research on the shared Mt. Elgon trans-boundary aquifer between Kenya and Uganda aimed at understanding its dynamics. Mt. Elgon is a Tertiary age mountain that straddles the Kenya-Uganda border and has a trans-boundary aquifer. This study investigated the groundwater chemistry and its implication on water management and human health. Physico-chemical parameters of water that included electrical conductivity, pH, and temperature were measured in the field and the major cations and anions were measured at the Central Laboratories of the State Department for Water. Geological mapping and identification of sanitary risks were undertaken during the field work. The study revealed that the concentration of cations and anions in the groundwater varied spatially and temporally. Abundance of these ions were in the order Ca²⁺ > Na⁺ > Mg²⁺ > K⁺ for most samples and HCO₃⁻ > Cl⁻ > SO₄²⁻ >NO₃⁻. Interpretation of hydro-chemical data suggests that calcium carbonate dissolution, halite dissolution, Ca/Na ion exchange and Mg/Na ion exchange are the major processes that control the ground-water chemistry. Chemical results indicate further that the groundwater is suitable for domestic use but is threatened by both anthropogenic and geological factors. Extensive use of fertilizer and the destruction of the catchment area coupled with low permeability and rock-water interactions in the metamorphic rock terrains are the main threats to groundwater quality in the region. A few water points had water with some ionic composition exceeding WHO and the local KEBS maximum limits for drinking water. Such water pose a risk to human health.

Kanoti, JR, Olago D, Opiyo N, Nyamai C.  2019.  An overview of groundwater and sanitation challenges in Kisumu City, Kenya. International Journal of Innovative Research & Development. 8(4) Abstract

The sub-surface is used in most parts of Africa as a repository of human waste and as a source of groundwater through pit latrines and shallow wells respectively. The wells provide freshwater to millions of people in Africa who are either not connected to the piped water or have intermittent supplies. These shallow wells are hand dug and therefore are mostly less than 20 meters in depth. This same sub-surface environment is also used as a repository of human waste through pit latrines. The water points and the sanitation facilities are mostly located close to each other. This study aimed at appraising the groundwater and sanitation challenges based on a rapid survey, sampling, interviews, existing literature review and historical borehole data in Kisumu city, Kenya. Previous studies in the area have shown that the number of shallow wells, city buildings, density of unimproved pit latrines and sanitary risks have increased tremendously between 1999 and 2019. Most of the wells are shallow and therefore prone to contamination by pollutants. Fluoride and chloride content in most boreholes are above the recommended WHO maximum values and the local KEBS standards. The study confirmed that the main water and sanitation challenges in Kisumu are poor and deteriorating water quality, poor waste disposal management systems and poor sanitation services. There is need for the introduction of new and sustainable groundwater approaches supported by scientific models and involving all stakeholders. Current deficiencies in the provision of adequate water and dignified sanitation to the poor in Kisumu can be remedied through improved knowledge on shallow aquifer dynamics and innovative research. It was noted that apart from the donor agencies and multi-national NGOs, the private investors are unwilling to invest in water projects in Kisumu due in part to government legislation that constrains the cost that may be levied on water

KANOTI, JR, Olago D, Opiyo N, Nyamai C, Dulo S, Ayah R.  2019.  Microbial and Physical Chemical Indicators of Groundwater Contamination in Kenya: A Case Study of Kisumu Aquifer System, Kenya. Journal of Water Resource & Protection. 11:404-418. AbstractWebsite

Safe water of adequate quantity, and dignified sanitation, is vital for the sustenance of a healthy and productive human population. In the recognition of this, the United Nations formulated the Sustainable Development Goal No. 6 to ensure access to safe water and sanitation by all by 2030. Actualization of this Goal requires information on the existing status of water resources and sanitation levels. Knowledge on contamination of groundwater is essential to prevent risks to human health. The objective of this study was to determine groundwater contamination in Kisumu, Kenya. A total of 275 water samples were collected from 22 sites within the informal settlements between December 2016 and December 2017. The samples were analysed for bacterial contamination and physical chemical quality. Thermal tolerant coliform bacteria enumeration was used as a proxy to bacteria contamination, and the pH, turbidity, dissolved oxygen, conductivity, salinity and temperature were used as physical chemical indicators of contamination. The results indicate that groundwater in Kisumu hosed coliform bacteria and therefore didn’t comply with contamination limits for domestic water proposed by WHO and local KEBS standards. The results further indicated that the levels of bacteriological contamination vary with water type, shallow well having the highest bacterial loads. The study concluded that there were potential risks to human health due to high content of coliform bacteria. The study attributed the contribution to pit latrines that were present in virtually all compounds. The pit latrines are located close to the water points. The study recommended the definition of minimum distance between the pit latrines and shallow wells to minimize contamination. The low income dwellers should be educated on simple ways of treating drinking water contaminated by microbial to minimize enteric infections.


Kanoti, JR, Olago D, Taylor R, Opiyo N, Nyamai C.  2018.  Situational analysis of threats to groundwater in the Lake Victoria Basin: A case study of Kisumu City, Kenya, September 2018. IAH Congress. , Daejeon, South Korea Abstract

Based on a five-town case-study cohort in Kenya, a conceptual framework has been developed to enable the formulation of holistic and effective strategies that encompass the national aspirations and regional to global sustainability agendas, and which can be used to monitor progress in achieving set objectives. The approach is flexible, scalable and transferrable, so that it can be applied in different contexts and using different indicators, based upon the same construct. Insufficient technical knowledge of urban aquifers and their interplay with the wider social-ecological system constrains the development of holistic, effective and robust management systems to ensure their sustainability for intended uses. The objective was to consider governance and management solutions that could promote water security for urban towns in Kenya through the sustainable use of groundwater in the context of its complex hydrogeology, water access disparities, competing uses and future risks. The in force national and county water policies, strategies, and plans for the case study areas were critically reviewed. The status of aquifer knowledge, water access disparities, competing uses, and risks was evaluated from critical literature reviews and data compilation, fieldwork, and analysis of indicator datasets from the Kenya 2009 census. Key aquifers need urgent characterisation to reverse the current situation whereby development proceeds with insufficient aquifer knowledge. Private sector and public participation in management should be enhanced through decentralised management approaches. Water infrastructure and technologies should be fit-for-purpose in application and scale, and the pro-poor focus should be underpinned by appropriately focused management regimes.


Olago, D, Dulo SI, Kanoti MJ.  2015.  Sustaining Urban Groundwater-Fed Water Supplies and Sanitation Systems in Africa. The Royal Society. Abstract


Kanoti, JR.  2013.  Investigation of Ground Water dynamics in the Lake Victoria Basin using Hydrogeochemical and Isotope Hydrology. , Nairobi - Kenya: University of Nairobi Abstract

Kenya is classified as a water-scarce country with per capita water being below the global benchmark of 1,000 cubic meters. In 2005 the estimated per capita was about 647 cubic meters for all uses. This scarcity is expected to worsen by 2025 when per capita is projected to be about 235 cubic meters. This poses a serious threat to socio-economic development, the integrity of national ecosystems and the quest to achieve the Vision 2030. There is therefore urgency to investigate and understand the available freshwater resources and water dynamics so as to formulate informed policy. This study targets the Nyanzian trough in the neighborhood of the freshwater Lake Victoria. This region faces a lot of water challenges related to water quantity, water quality deterioration, transboundary water issues and perennial flooding.

To counter the challenges, we need to improve our understanding of the water cycle since it is one of the key elements of scientific information necessary for developing policies toward a sustainable management of freshwater resources. Water supplies in the area come from various sources including surface water, shallow and deep wells.

The aim of this study is to investigate the groundwater characteristics using suitable environmental isotope techniques in order to establish the links between groundwater and the surface water for better exploitation strategy. It will investigate and demonstrate if there is any link between the lake water and the boreholes and if water mining is occurring in some regions within the basin.

This study also aims to answer local hydrologic questions about the aquifers through studies with pumping tests and stable isotopes. Specifically, of interest is the amount of dispersion in the deeper aquifer, its degree of hydraulic connectivity, and whether there are signs of younger, shallow groundwater intrusion. On a regional scale, we would like to know what the age and recharge rates of groundwater are at depth, thus allowing the estimates of groundwater flowlines and their changes with shifting deep groundwater usage.

The study will explore the near-surface processes of the land phase of the hydrologic cycle (surface and shallow subsurface processes) in particular the movement of water near the earth's land surface, the physical and the chemical interactions with earth materials accompanying that movement.
Flow system analysis and tracer hydrology will be used to evaluate the water resources within the basin.

This will involve determination of the characteristics of the natural groundwater flow field, flow systems and hydrogeochemical facies analysis of water samples. The definition of the facies and classification of water types in the basin including identification of groundwater origin will be undertaken during this study.

Different methods of analyses and assessment of hydrological flow systems will be used including hydro-chemical and tracer hydrological approaches to delineate flow systems and understanding flow patterns in the Basin. The use of tracer techniques will illustrate the flow pathways, residence times of the water, the hydraulic properties of flow systems, and the mixing of different water compartments if any.

It is envisaged that through this study the general use and acceptance of hydrogeochemical proxies and by extension, isotope methodologies into the mainstream hydrology and water resources management in Kenya will be adopted since isotope techniques may provide, among others, adequate information on recharge conditions, quality and age of groundwater. It may also unravel the role groundwater dynamics contributes to the Lake Victoria waters and to the flooding in the Basin.


Kanoti, JR.  2012.  SUSTAINABLE URBAN DRAINAGE SYSTEM: NAIROBI CASE STUDY, 8th June,2012. Submitted during the Sustainable Communities Course: Urban Environmental Management. , Bangkok, Thailand Abstract

One way of dealing with urban floods is to ignore them. In many countries, Kenya included, neither the people nor the authorities want to take the danger due to urban floods seriously, partly due to large recurrent intervals of most urban floods. It may also be that the risk due to floods are taken for granted, given the many dangers and problems confronted with in people’s daily lives (Van Westen, C.J., 2000 ).
To effectively reduce the impacts of floods in our cities, including Nairobi, they must be managed before they turn into disaster. The primary objectives of sustainable urban drainage system can be considered to be the protection of life, property, the community and the environment. The process comprises a series of well-known stages, which begins with urban drainage evaluation. The second stage involves the evaluation, selection and implementation of flood reduction measures, and the establishment of enforcement procedures. This stage links urban flood management to emergency planning and management that are subsequent stages of the process. Preparedness, response and recovery are the three principal stages within emergency planning and management. The final stage in the flood management process is the feedback stage, where post-event appraisal of mitigation measures and other phases are evaluated (Starosolszky, O., and Melder O.M., 1990).
The sustainable urban drainage management process is open to institutional arrangements and policies, political economy and the technological environment. These influences exert both positive and negative forces on the drainage management thereby making it either effective or ineffective. The nature of hazardous environment need not be overemphasized because it determines the need for management. To make the process smooth, public cooperation is needed.


J.R.Kanoti, B.  2002.  EXPLOITATION OF MINERALS IN THE TAITA TAVETA RANCHES, 2002. Ranchers and Related Stakeholders workshop for Taita Taveta District. , Mwatate Abstract

Throughout the world, prospecting for gemstone deposits is largely a primitive operation that does not involves scientific or systematic methods. In Taita Taveta district, most gemstones deposits are still found either by luck, or by direct visual inspection of outcrops or of the soil surface. However a wide range of methods are available to the prospector.

Prospecting methods include geological mapping, systematic eluvial test pitting, geophysical and geochemical prospecting. Remote sensing can also be used. It is important to understand perfectly the geological characteristics of gemstone deposits in order to be able to select the most efficient methods. In Taita Taveta, the combination of direct mapping, spectroradiometry, and soil geochemistry enables to delineate lithologies favourable to some gemstone deposits. On a local scale, computerised treatment of data obtained from systematic test pitting can assist in identifying possible secondary deposits, and to locate primary deposits.



The aim of this study was to investigate the detailed geology, the geochemistry and the mineralogy associated with the mafic and the ultramafic intrusives of the Mozambique Belt, eastern Kenya. To achieve this, a detailed geological mapping and sampling of the intrusives was done followed by laboratory analysis. The significance of the study was to highlight the nature, relative age and genesis of the intrusives and the potential for economic mineralization.

This study has revealed that the intrusive rocks and the regional foliation trends are inter-related suggesting that the intrusives developed in vertical structures during regional metamorphism. The elongated shapes of the bodies and their alignment with the enclosing regional structural grain of the gneisses suggest compressional deformation during the regional Mozambique Belt Orogeny. This is considered as evidence for at least a synorogenic emplacement of these intrusive rock bodies.
The mafic and the ultramafic rocks represent a range of differentiated rocks from fairly primitive magma (Mg-number = 79) to highly fractionated magma (Mg-number = 36). However, the fact that the rocks are intrusive brings out the possibility that none of them may represent parental magma composition. The magmas have undergone modification by crystal fractionation processes either in high-level magma chambers or during ascent from their mantle source regions. The gradual composition change in the feldspars, olivine and the pyroxenes is from high- to low-temperature members of their respective solid-solution series. This outlines the crystallization sequence.

The whole rock chemical analysis shows that rocks rich in magnesium oxide are also rich in chromium and nickel and those rich in potassium oxide are also rich in rubidium and barium in conformity with the rules of partitioning. This implies that they originated from one parent magma. The rocks show iron enrichment trend and have high nickel and low aluminium oxide contents. This chemical evidence supports a tholeiitic magma affinity for the intrusive rocks.
An attempt is made to construct the mineralogy of the gabbros based on the mineral chemistry. This has revealed that they are composed of magnesium-rich olivine (chrysolite) with approximately 80% forsterite. The pyroxene is both magnesium and calcium rich and has an enstatite molecular percentage of about 18%. It is an orthopyroxene (bronzite) in the enstatite-ferrosilite solid-solution series. The plagioclase feldspars show a range of composition from about 90-20% anorthite. This
range shows that the magma crystallized slowly. Crystallization over a wide temperature has resulted in the formation of alkali feldspars and other minor constituents.

Economically, the area has the potential for base metals. Chromium and nickel are present in concentrations higher than that found in average igneous rocks. Further geophysical work is recommended to reveal some more information in terms of the possibilities of economic deposits in this project area. Some of the pegmatite, particularly those near Muthanthara contains small needles of beryl. The beryl is blue green in colour but not of gem quality.


KANOTI, JR.  2000.  RIVER FLOOD HAZARD MANAGEMENT IN THE NETHERLANDS - A REFERENCE FOR KENYA.. , ENSCHEDE, THE NETHERLANDS: International Institute for Aerospace Survey and Earth Sciences Abstract

Throughout history man has been attracted to the land adjacent to rivers. The soil is normally fertile, there is a constant water supply, it is a cheap means of transportation etc. Settlements along or beside rivers are however hazardous. Once in a while, the rivers may overflow their banks and inundate the built up areas resulting in damage to crops and property, and sometimes loss of life as well.

Netherlands is worldly renown for its fight against floods. Therefore other countries can emulate a lot. The study tried to investigate the flood control and management practices in the Netherlands, and the feasibility of applying some of the methods to a developing country like Kenya.

From the study, the importance of good institutional framework is exemplified. A clear definition of flood management policy is essential if a country is to establish and maintain adequate arrangements to deal with floods.

In identifying what options are available as elements of national policy, it is useful to study all aspects of hazard management, namely; prevention (mitigation), preparedness, response and recovery. As one African saying goes, prevention is better than cure. But due to the social-economic constraints and engineering feasibility problems, some mitigation measures are beyond the reach for many developing countries. Therefore structural mitigation measures are not the most cost-effective methods for solving flood problems. The best methods are non-structural since they involve little costs and are more sustainable. Preparedness, response, and recovery must be covered in national policy to the best possible extent through government decrees, statements, legislation, regulations and other means.

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