My borehole is contaminated. What can I do?

If you have ammonia or e coli in your borehole supply it could well be due to pollution by sewage (groundwater is very unlikely to show these types of pollutants due to other causes). This could be either from run off from agricultural land, or from a human sewage outflow.
 
In the long term it would make far more sense to prevent your water being polluted in the first place rather than trying to remove the ammonia and the coliforms. There are various ways in which your borehole could be getting contaminated. Are the headworks of the borehole (the bit that hits the ground surface) raised above the ground and fenced off, or is there a possibility that surrounding surface water is entering the borehole at the point you are abstracting from? The Environment Agency have various leaflets on managing water abstraction; I would recommend you asked them for the one called "Water Supply Borehole Construction and Headworks. Guide to good practice." This has got some good pictures of how boreholes should be constructed to avoid contamination.
 
If it isn't being contaminated from your abstraction point, then you should try and find the source of the contamination. Is anybody else abstracting water nearby from the same aquifer? If so, have they had their water tested and does it show similar contamination? Are their borehole headworks of a suitable standard? Depending on the depth of the aquifer and the nature of the geology it is possible that the source of the pollution is very diffuse and agricultural, rather than a point source at an individuals borehole, although it's difficult to tell without getting an expert to look at the site.
 
If you can discover the source of the contamination and prevent it occurring, you should then be able to sterilise your borehole to remove any final contaminants, and then you should be ok.
 
It should be possible to install a treatment system for less than £2000 (although it depends on the levels of contamination and how much water you are trying to filter), and in any case, prevention would be a far better approach; stop the water getting dirty in the first place rather than clean it once it's been made dirty. 
 
If you haven't already done so, I recommend you talk to your local Environment Agency officer for water abstraction; if local groundwater is being polluted with sewage, be it due to agriculture or humans, they will want to know about it so they can take remedial action (but you should read the EA publication on boreholes first just to make sure that it isn't your fault the groundwater is getting polluted!).

Contacts

CAT Consultancy: Eco Sanitation - http://content.cat.org.uk/index.php/water-and-natural-resources-consultancy - email: consultancy@cat.org.uk
  CAT experts offer detailed technical advice on composting toilets, reed beds, septic tanks, leachfields, water filters, water conservation, water reuse, rainwater harvesting.
Environment Agency - http://www.environment-agency.gov.uk - 0870 850 6506
  Public body responsible for protecting and improving the environment and to promoting sustainable development.

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