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We have a well (about 1200KM away from sea and 60 meter deep), the water when taken out has slightly dark color and has smell. But strangely in about 12 hours the smell and black color vanishes and water becomes odorless and clear without leaving any residues.

What can be possible cause, are there any known underground impurities that change with something like sunlight or air exposure?

Organic impurities and sulfides don't disappear like this, can someone help with details of this kind of water impurity.

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    $\begingroup$ the type and depth of the well, and the local geology will make this answer a lot easier to answers. The possibility of caves, seawater, and a hundred other thing come into play. $\endgroup$ – John Dec 8 '18 at 23:36
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    $\begingroup$ Usually black stuff and smell mean either (1) organic matter, or (2) sulfide compounds. It's hard to say anything more without more information. $\endgroup$ – Gimelist Dec 9 '18 at 5:16
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    $\begingroup$ can you take a water test(you can buy it at a pet shop in the form of test strips) the most interesting is the PH and how hard the water is,the amount of nitrates and if there is any chloride is of interest too.please take two tests one straight from the well and the other after 12 hours. $\endgroup$ – trond hansen Dec 9 '18 at 17:50
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    $\begingroup$ A small amount of hydrogen sulfide can make a very bad smell that dissipates quickly. $\endgroup$ – blacksmith37 Dec 9 '18 at 20:41
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This is due to the presence of iron sulfide in the water. The iron sulfide oxidizes and goes into solution. Ferrous iron oxidizes to ferric iron. Depending on the water chemistry, this commonly precipitates out as orange-coloured iron oxyhydroxide, but that does not seem to be occuring in your case, otherwise you would see it. When it does happen, the pH of the water drops, as seen in acid mine drainage.

The sulfide may be volatilized as hydrogen sulfide which smells, or it too may oxidize and volatilize as sulfur dioxide (rotten egg smell). It can continue to oxidize to sulfate.

The iron sulfide may be present in the aquifer or it may be formed by microbial activity in your well. In the latter case, treating the well with bleach can solve the problem, at least temporarily. Be sure to treat all the piping, too. If possible, install a backflow preventer so water doesn't flow back down the well.

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    $\begingroup$ Generally H2S is formed by microbial action adjacent to wells ; quite a problem for the petroleum industry. $\endgroup$ – blacksmith37 Dec 10 '18 at 17:29

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