20 May, 2024


Bore-Wells & Salinity In Jaffna

By Willie D. Joshua

Willie D. Joshua

Willie D. Joshua

Danger of soils becoming saline from bore-wells water in the Jaffna Peninsula

Fresh water supplies and arable land are at risk due to indiscriminate digging of bore wells resulting in saline water extraction. Simple methods for mapping the depth of usable water are proposed that can be used to guide well-depth and prevent significant environment degradation. This information can also be used to estimate the available groundwater for human use.

Recently, there has been a trend in drilling bore wells in the Jaffna Peninsula to extract groundwater for domestic use. This practice is to be implemented for houses being built with foreign aid to settle displaced people in the war torn area. These wells are constructed by drilling about 15cm (6 ins) circular holes right down to the groundwater. The water from these bore wells is used directly by hand pumps or is pumped to an overhead tank and distributed by pipes within the house for domestic use. The groundwater in the peninsula consists of a fresh water layer underlain by salt water. There is a danger that if the bore well goes down to the depth of the saline layer, the pumped out water will be brackish. Thus, there is a possibility of good land becoming saline if this water is used. There have been some instances in Jaffna, where the waters from the bore wells are brackish and not usable even for domestic purposes. Therefore, the depths of the bore wells have to be above the saline groundwater. The Northern Provincial Council has already been informed of this potential problem and remedial measures also have been suggested. Bore Wells

There are three types of wells in use in Sri Lanka namely agro-wells, tube wells and bore wells. Agro-wells, also referred to as dug-wells, are the ones commonly in use in the Jaffna Peninsula and elsewhere in Sri Lanka. Water from these wells are used both for domestic and irrigation purposes. These are large diameter (2-3m) wells whose depths do not go beyond 1m below the dry season water table.

Tube wells are similar to bore wells. They have a 15-20 cm diameter, but go to a depth of more than 70m (200 ft) to tap the deep aquifers of limestone and sandstone. These tube wells are found in the western areas along the Mannar-Pooneryn road.

Bore wells, as described earlier, are the shallower version of the tube wells. They tap only the groundwater formed by the percolated NE Monsoon rains. The need for bore wells arose because the cost of constructing the usual agro-wells has risen sharply. Another reason is houses in Jaffna are being built in small compounds, and there is lack of space to accommodate a large diameter well. In the 1970s and 1980s, people in Jaffna drilled bores of very small diameter of about 5cm (2 in) at the bottom of their agro-wells in the hope of intercepting some dissolution channels or cavities in the limestone aquifer to increase water supply in the well. Fortunately the waters were not brackish. Presumably, these drill holes were not deep enough to make the water brackish.

The large diameter agro-wells have been in use for a long time, and are preferred because a considerable volume of water is recharged and stored in the wells between the irrigation intervals of few days. This stored water itself is was often sufficient for irrigation. As the wells are shallow, most of the recharge of water would have been from the non-saline surface layer of the groundwater.

The officers who are responsible for authorising the construction of bore wells appear to be unaware of the saline water always present below the fresh water. If they knew the depth at which, for any particular location, the ground water becomes saline and unfit for human use, they could specify the maximum depth to which bore wells should be constructed in order to avoid salinity. Unfortunately, this information is still not available for the Jaffna groundwater.

Formation and quality of groundwater in Jaffna Peninsula

The limestone bedrock of Jaffna, with its large pores and cavities, extends below sea level and functions as an excellent aquifer (water bearing porous material). Even sands in the Vadamaradchi area act as an aquifer. These aquifers are charged annually by the North-East monsoonal rains between October and January. The rainwater percolates downwards through the soil and moves into the pores and cavities of the limestone/sands. The percolated fresh rainwater forms a layer within the aquifer and floats on top of the denser sea water that is already present in the aquifer at sea level.

According to the Ghyben-Herzberg Principle, the weight of the fresh rain water pushes down the denser sea water so that the overlying fresh water is in the shape of a convex lens within the porous limestone. The fresh water level (water table) has to be therefore above mean sea level. In reality however, the lower part of the fresh water lens is actually a transitional zone where the salinity level of the fresh water layer increases gradually with depth from fresh water at the surface to that of sea water at a lower depth. Therefore, the usable fresh water actually is the upper part of the lens that is formed by the rainwater.

The usable upper part is the depth up to which the brackishness (salinity) of the groundwater is low enough and fit for human use. Generally, the usable fresh water is considered to have salt (chloride) content lower than 500 parts per million. The thickness of this layer of good water is variable; depending on the location, season and the extraction rate. Usually, this usable water is thicker in the centre of the peninsula and becomes thinner towards the coast. In order to maintain the freshwater lens, there has to be continuous outflow of water from the lens to the sea, even though becoming slower with time. Consequently, the fresh water lens becomes thinner with the progress of the dry season and usage. The fresh water lens, although becoming thinner, has always been present till the end of the dry season.

As described above, all aquifers in the peninsula will always have fresh water in the upper layer followed by the transitional zone of increasing brackish water. In all probability, individual aquifers are present in the three landmasses (Valikamam, Thenmaradchi, Vadamaradchi) separated by the lagoons and also in the Islands. The quality of water in the wells will depend on the thickness of the fresh water layer and whether the bottoms of the wells are in the fresh water part or in the brackish part. Since the thickness of the fresh water layer becomes smaller towards the coast, the depth of wells have to be finely judged to intercept only the fresh water layer to the middle of the lens to keep the water always fresh. As a rule, coastal wells, whether they are in the peninsula or in the islands, have to be shallow in order to avoid salinity. A good example of this situation is the well located on the island close to the Jaffna Lagoon, in the compound of the Catholic Church in Charti. The well is shallow and the water is always fresh.

Very often, people dig or drill deeper wells to get more water but end up only getting brackish groundwater. Even pumping tests in shallow fresh water wells are meaningless because even little excess pumping may bring up the underlying salt water like a cone. There is an urgent need to determine the thickness of usable freshwater (the upper layer of the lens with chloride content less than 500 parts per million) and its depth variations with the progress of the dry season.

Remedial measures to avoid salinity

It would be greatly desirable to estimate the depth and its variation of the usable fresh water at different locations in the Peninsula. This information not only helps to determine the permissible depth of bore wells, but also helps to reliably estimate the total amount of water available for human use. There are many methods available, both physical and electronic, to determine the depths of usable fresh water in the lens.

1. Physical measurements: In principle, it is possible to establish a network of deep boreholes of small diameter, in a grid at regular intervals in the peninsula. The groundwater in the bore holes are measured periodically for water table depth and salinity. This will yield information on variation and depth of the usable water in the lenses for the entire peninsula over the seasons. The details of the actual procedures have to be worked out. There are already many boreholes drilled in the peninsula for previous studies, locations of which may be available with the Water Resources Board.

2. Electronic measurements: Radioactive and electronic techniques exist that may be applicable, but the author does not have the relevant expertise to explain the methods in detail. However, any instruments used for either electrical sounding, radar or gamma ray methods need local calibration, as manufacturer’s calibration has been found to be unsatisfactory. Several identified bore holes that are in the peninsula from earlier studies can be used for this purpose. In 2006, a detailed study was undertaken by SMEC International Pty Ltd on groundwater of some locations in Jaffna. The boreholes in this study have all the information regarding relief, coordinates and borehole drilling log etc. SMEC has identified electronic equipment that could be used for identifying salinity levels at different depths of groundwater without actually drilling boreholes. The reports are available at the office of National Water Supply and Drainage Board, Jaffna. This information has been passed on to the Northern Provincial Council.

It is the author’s urgent recommendation that those responsible for management of water supply in the Jaffna peninsula, namely the National Water Supply and Drainage Board or the Water Resources Board, take immediate action to map the depth of usable freshwater in the Peninsula, and use this information to guide the regulation of new wells. The persistent digging of too-deep wells caused by ignorance will result in an inadequate supply of fresh water and irreversible salinisation damage to good land, jeopardising the future liveability of the Jaffna peninsula. Prompt, simple action could prevent a major environmental disaster.

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Latest comments

  • 3

    Thank you for the timely reminder.
    This matter has been talked about before and this article is most useful.
    There is also serious need for Jaffna to return to to rain water harvesting and water conservation projects.

  • 2

    It is a timely article by a knowledgeable person. Thank you very much. I too did not know much about these water table. But I know too deep boring will bring saline water into the tube and supply salt water. This is exactly what is happening in the islands. In fact I too paid for a tube well and closed the agro well as the water got was from my well was more or less from a depth of about 20-30 feet. I thought drinking that water might be not safe in view of water seal lavatories with pits being constructed practically in every houses in Jaffna from where seepage might trickle into such wells. Of course we test the water for any pollution. How many can afford such tests. Therefore to be scientific is safe and economical. Will the Northern provincial council provide the guidance as suggested by this author.

  • 4


    Would a ‘Jaffna River’ help provide larger quantiles of low salinity fresh water tapped through agricultural. Tube and bore wells for domestic and agriculture use?

    I notice that the quality and quantity of the water in the two wells in our property tremendously improve after rains and when the nearby lagoon is full.

    Dr.Rajasingham Narendran

  • 1

    when the water is lost the water pillars holding the land will crumble and the surface go down in salt water along with all the high security zones.

  • 0

    Thank you for your continued interest in commitment Jaffna and Jaffna matters

  • 1

    very useful at the moment when a large number of houses are going to be built.

    There must be a group of informed people working to change the Jaffna habit of having a well in each house to having a well for a group of houses. With govt planning that group can be big with attendant structure.

    These people must be involved in this?
    IWMI Headquarters and Regional Office for Asia
    127 Sunil Mawatha, Pelawatte, Battaramulla, Colombo, Sri Lanka

    So that the readers can make the most of the published material:
    Pl state who the author is , esp when such serious matter is written.

    • 1

      For those interested in the topic:
      Assessment of Groundwater Resources in Jaffna Limestone Aquifer, M. Thushyanthy( Department of Agricultural Engineering University of Jaffna, Jaffna Sri Lanka) and C.S. de Silva (Faculty of Engineering Technology, The Open University of Sri Lanka, Sri Lanka ). Tropical Agricultural Research Vol. 23 (2): 177 – 185 (2012), file:///C:/Users/PS/Downloads/4649-16553-1-PB%20(2).pdf

  • 1

    Dr. Rajasingham Narendran

    Probably the bottom of your wells are at such a depth, that during the rainy season, they are within the thickness of the fresh water layer. During this season, the lagoons are also full and less brackish. During the dryer season when the fresh water lens become thinner, bottom of the wells intercepts transition zone which can be at different degree of brackishness. Water at sea level(even lagoon water), whether fresh or brackish, cannot recharge the groundwater formed in the aquifer
    River for Jaffna is a different concept. It has to take into account free water evaporation, surface storage, exclusion from sea etc.

    Willie D. Joshua

    • 1


      Thanks. Our wells are not deep- they may be 10-12 meters deep. One is broad and the other narrow. We always have water. In the hot season however, the water becomes a little more saline.


    • 3

      Mr. Joshua

      It was very interesting to read your article on groundwater conditions in Jaffna and the surrounding Peninsular. I myself as a practicing geologist, thought of supporting and strengthening your suggestions.

      I understand that the major aquifer in northern part of Sri Lanka is the Miocene aged partly fossiliferous limestone and main chemical composition of the limestone is calcium carbonates (CaCO3). This bedrock therefore tends to be highly porous and may have numerous interconnected solution cavities (geologically known as karstic features) due to dissolution of calcium carbonate in the rockmass over prolong period in the island’s geological history. Therefore mass permeability of this rockmass is significantly higher than permeability conditions of much older rocks underlain in rest of the island. It is believed there may be a network of underground stream systems connecting these features even extending into deeper oceans. Such observations were fully documented in literature with similar geological terrains and ground conditions.

      My understanding is that the above mentioned underground network could be even dry, partially filled or totally filled with fresh monsoonal rain water to ingresses saline water or combination of both depending on the climatic conditions of a period and subsequent extent of seawater ingress through. As you outlined in your article, I fully agree that hydrogeological characteristics and groundwater conditions of the limestone rockmass in this part of the Island has not perhaps been fully understood by the local groundwater experts. It needs a detailed study in order to understand and remediate current brackish water ingress problems and ongoing groundwater contamination issues of the Peninsular’ s due to both natural and human activities.

      Thanks once again for your comprehensive and valuable article.


      • 1

        Awith Dissanayake,

        Thanks for your input. From what I understand, in vast deserts of Saudi Arabis too there are huge reservoirs of of various levels of TDS and underground streams that flow in from even Syria to replenish them. However, under the much touted program to achieve food self sufficiency, the depletion rate was higher than the replenishment rate.

        From what you at the moment guess about the situation in the Jaffna peninsula, could I assume that the likelihood of the replenishment of acquifers from surface penetration is high. The water management system of old consisted of rain retention ponds of various sizes to permit percolation of the stored waters into the acquirers.

        Your further thoughts are welcome.


  • 1

    Willie de Joshua

    Thank you for your scientifically proven water Salinity disaster awaiting to happen.

    Very well timed article to high light the necessity In doing so in avoiding future catastrophe in the North or anywhere else in the country.

    As you say it has become a fashion to obtain Bore wells as its space saving and prevention of well water getting contaminated with poisonous pollutants due to nature or by by fowl means.

    Please Educate the public of this and how to prevent future catastrophes and preserve the future generation from the effects of this.

  • 5

    Not only Saline problem but also the total water management in the Northern province need multidiamensional approach. The intensive cash crop based agriculture has played significant contribution towards poor water quality including including salinity, water pollution, health related issues etc.

  • 3

    The urgent solution to this water issue is that the Northern and Eastern Province needs a central Water and Wastewater Recticulation Schemes, based on the size of the districts and population. The management, operations and maintenance of such schemes should be the responsibility of the NPC/EPC.
    These schemes should replace and phase out All bores and waste and septic tanks, as soon as possible.

    In the meantime All bores, domestic, commercial or for agriculture should be licenced with strict conditions on the depth, the amount of draw or the size of the pump to be used. Some bores should be metered to prevent abuse.

    With a Jaffna river, dams, compensating basin and proper drainage will assist to replenish the ground water table and if managed properly will provide continuos supply of good drinking water.

    This project is serious as suggested by the author and should be treated as an urgent project and require international funding and local leadership.

    Manicka Vasagar

    • 3

      I agree with you. The North East Provincial administrations needs to play a key role in bringing changes towards better management of land and water resources. A politico-socio-economic and technical approach is essential. We need to separate out our agricultural, Industrial lands from rest of the lands for housing and city development. Agricultural sector needs very strict legally adopted proceedures and technically sound and efficient methods and practices, particularly in the use of water and chemicals.

      The saline problem under tube well based settlement schemes (Mulankavil, Vellankulam) was noticed in 1980s. Recently digging of tube wells in Jaffna has grown exponentially with out any restrictions and if that continues, the saline problem is enough to wipe out Jaffna.

  • 1

    sarcassm is clearly evident.

    yes, Mr. Willie Joshuwa satrted the subject matter.
    Ajith Dissanayake man on the topic currently weighed in but nobody was interested add a comment to AD to rectify or work or move into the matter further to rectify issues.

    is this attitude a mentality dis-order?

    thank you AD for your input.

  • 0

    Well thought and well written, the first step for any planning is assessing the current status of (fresh water) resources. Electric resistivity method is a very simple technique, widely used in exploration of subsurface mineral and water. It is used here in Sri Lanka too. A study titled “Subsurface geological and hydrological conditions of the Matale District: Inferred from vertical electrical sounding curves” is on web. I happened to work on my colleagues M.Phill thesis quite a few year before. As I remember, he did the survey at Mundal, Puttalum District. He had assessed the fresh water resources and established the dynamic of salt water- freshwater interface with dry and wet season.

  • 2



  • 0

    Some of you may be familiar with Dr. Joshua’s article
    “Joshua WD, Thushyanthy M, Nanthagoban N (2013)
    Seasonal variation of water table and groundwater
    quality of the karst aquifer of the Jaffna peninsula-Sri
    Lanka. J Natn Sci Foundation Sri Lanka 41:3–12

    from three years ago.

    The trend away from agriculture, and towards hosing should
    DECREASE the amount of projected water need of the future.

    In the NCP, people built many many tube wells in the 1980-1999s
    with foreign NGOs taking the lead. Unfortunately, more than
    2000 of them had to abandoned as white elephants, because the
    water drawn from then became charged with geological minerals,
    raising the ionicity (i.e., salinity due not only to salt, but due to other salts).
    There was very little testing or a scientific approach by these INGOs.
    I think ultimately some rules and guide lines about building tube wells
    were put in around the year 2000 – after much waste.

    In Bangladesh the INGOs (even with the support of the UN)
    installed tube wells without chemically analyzing the
    underground water. This led to the bringing up of arsenic
    containing water, and causing a huge man-made arsenic toxicity and
    kidney disease. It was only after the epidemic of kidney disease
    that they proceeded to analyze the water! The cry that there is
    arsenic in the NCP water, and causing CKDU probabaly came from
    that knowledge, but today we know that there are no
    significant amounts of heavy metal toxins like
    As, Cd or Pb in the the NCP water, and also in the water
    table of Jaffna (according to a Japanese study).

    The famous water Engineer Arumugam was one of the pioneers who studied
    the lime-stone aquifer system in the peninsula. A project known today as the
    “Rivers for jaffna” project was proposed in the 1960 as the “Arumugam plan”.
    The first two parts of the project (involving the building of barrages) have
    been completed.
    The last part which involves the ambitious concept of bringing water
    from the Vanni to maintain an artificially created “freshwater lagoon”
    has not been achieved. It involves building a spill plus causeway
    of about 2100 metres long and a bund of 1400 metres long, to
    convert the ElephantPass lagoon into a fresh water lagoon, cutting it off the
    sea by the bund. Then a canal has to be cut to take the water to Vadamarchchi
    and Upparu. The hope was to cultivate some 4500 hectares (bordering the Vadamarachchi and Upparu lagoons) (which are are un-cultivatable due to a brackish water table) by making the land eventually free of salinity. In the 1960s there was the idea of even growing tobacco, but today that is not the objective.

    I used to be enthusiastic about this project in the 1970s, but today I am not so sure. The people who currently use the brackish land for prawn, crab and marine fishing will loose their livelihood. If the land becomes free of salt, it will be new developers who will take over the land and exploit it, ejecting the poor people. Furthermore, experience (e.g, in USA where attempts to convert salty lagoons to freshwater lagoons) has shown that it takes decades and decades to leach out the salt from the soil. Lagoons right next to the sea, even if pumped with fresh water, never really become fresh, due to ingress of salt water from the bottom of the lagoon where there is no underlying lens of freshwater in an aquifer. That is indeed the case under the Elephant Pass lagoon. My fear is that we may end up with neither a salt water lagoon, nor a fresh water lagoon, but an expensive brackish water lagoon. So, I hope that modern day engineers and environmentalists should re-examine this important part of the Arumugam project using modern environmental assessment methods. It is an essential tribute to a great engineer and water scientist like Arumugam, that we must ensure that his plan does not end up in environmental disaster or create a state of partially leached brackish land that fails to realize the initial objective of cultivating the land.

    Furthermore, in the 21st century, the future of the Jaffna peninsula may have to be thought more in terms of huge urban-water needs, with agricultural needs taking a mere second place. This is a pity, since one should grow one’s own food in one’s own locality as far as possible. But this may not be so even for the Jaffna penisnula of the future that may be inundated by south Indian migrants and workers, if the proposed land bridge to India is built. Then the jaffna peninsula will look like a poor, densely packed suburb of Chennai, say, like like Tambaram.

    • 0

      Thanks for focusing on the Jaffna River project and identifying a potential problem. Engineer Mendis, an ardent advocate of this project and who has fought many battles for it, should respond to this new concern. I hope he does so soon. Those who know how to contact him should invite him to comment.

      I listened to his lecture 2-3 years back on the subject and was convinced of its feasibility.


      • 0

        I have brought this matter to the attention of sevarl people including DLO Mendis, when Mendis wrote to me about it. I asked the latter to get an environmental impact review; but unfortunately this has not been done.
        DLO’s approach to everything nowadays is, I am afraid, based on nostalgia, emotion and simplistic marxism , rather than going at it scientifically. In the 1960s, when the project was proposed, someone argued that even if the water became brackish, it could still be used for tobacco growing. But that is out in today’s context. However, environmental assessment methods today are far more advanced and people can assess the problem by evaluating the sea-water seepage into the lagoon by simple experiments. Other aspects of the environmental impact must also be evaluated. This is a real problem that can be sorted out and fixed.

    • 2

      Much work on the Jaffna River project was done by The Mahinda Rajakase government soon after the war. The damage
      In terms of restoring the barrages. Further the Elephant Pass lagoon had been totally cut off from the sea by the army during the war. What remains to be done is only the construction of a four km canal connecting the Ekephant Pass to the Jaffna lagoon system. Even if the Mahaweli waters do not flow into the Irranaimadu tank, the Elephant Pass could become a large fresh water reservoir with the rain water and overflow from this tank.

      Please read the following link:


      Other very useful articles and studies on the subject can be accessed through a Goigle search.

      The Elephant Pass lagoon and the Jaffna laggons have been cut off from the sea at least for five years now. I have also pointed out in an earlier comment that the wells in my property that lies near a lagoon in Jaffna, have plenty of reasonably good water, when the lagoon is full.

      No one has explained to me yet why the short connecting canal should not constructed! Can someone do this, please?

      I think enlightened action should be taken to complete this project or completely rule it out, because foolish local initiatives such as the building of a cemetery in the middle of a lagoon, may destroy the likelihood of this project , which should be renamed ‘Project Hope’ for Jaffna ever coming to life.


  • 0

    Fantastic collective inputs from Intellectuals.
    Hope AD is following these information.

    Wish something good comes out from these inputs.

  • 0

    I have read the article and have been following the comments as and when they are posted. The article is very clear as far as the reasons for salinity, the need for action and the suggested remedial measures. The expected comments would have been towards the validity of the reasons and the applicability of the suggested remedial measures or new and better suggestions. Other comments could have been confined to the topic of bore wells and associated salinity problems. In this way a clear indications could be given to the Northern Provincial Council or other relevant authorities to take any necessary action immediately
    Latest comments have deviated to the River for Jaffna project which apparently was started in the early sixties. In reply to a comment, the author has said it is altogether a different program. I too think that the River for Jaffna should be taken up separately as there have been different opinions, valid objections and changes to the project. This is clearly reflected in the comments by Mr. Chandre Dharmawardene

  • 1

    Dr. Rajasingham Narendran
    As answer to your question on your well depths; It is exactly for the same reason I am advocating the remedial measures. In my article, I have clearly indicated that with the progression of the rainy season, the water table will keep on decreasing and the thickness of the lens will decrease ie. becomes thinner. Also the lens is thinner towards the coast. Consequently the transition layer, together with the fresh water layer of salinity less than 500 ppm of chloride at the surface of the lens, will also become thinner. As a result, the transition water level rise and affect the well water.
    In all probability, your well must be closer (relatively speaking) to the lagoon where the transition zone rises into the well. We have to know the locations in the peninsula in a grid where the depth of the fresh water lies in the driest month –August. For each unit of water table decrease, the sea water inter-phase of the lens at the bottom rises by approximately 33 units according to density differences.

  • 1


    Thanks for your response and explanation.

    Our wells are within about 500 meters of the lagoon shore. Your explanation establishes a direct relationship between the levels of water in the lagoon and the water levels in atleast in the proximal wells. Further, it establishes that higher rain water diluted levels of lagoon water, will reduce the salt content of the well water, at least in proximate wells.

    If my understanding is right, the Jaffna River project will prove beneficial to the people living around the rather the long lagoon system in Jaffna. Further, the concerns regarding the impending water crisis in Jaffna, in terms of human consumption and agriculture, should prove weightier than the ecological concerns being expressed. Further, the potential to reclaim 11,000 acres of land for agriculture, recreation and tourism will be an added incentive.

    The Jaffna lagoon system has been isolated directly, at the land surface level, from the sea for atleast five years now and thus has very likely less salt content. Further, although the underground connections to the sea will always be there, the ingress of sea water will be controlled by the surface water pressures. Concerns such as effects on prawn fishing are red herrings. We can always for fresh water fish and shrimp farming in the ‘Jaffna River’.

    The other explanation I seek is why the waters in wells around Chaatti beach in Mankumpan are of high quality and fit the term ‘Sweet Water’. It is a joy to drink this water.

    I think the completion of the Jaffna River Project is an urgent priority.


  • 0

    Dr. Rajasingham Narendran
    an error in the reply to you. It should read “with the progression of the dry season” instead of “progression of the rainy season”
    Sorry for the error

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