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Generally groundwater has been regarded as a better source of water in terms its low biological contamination and so have been favoured for this reason. However, there may be other contaminates that can make it less desirable.

I have just been looking into the issue of arsenic contamination in groundwater in Bangladesh which has led to a return to the use of surface water sources. Other contaminates from groundwater might be iron, fluoride, manganese, salts and nitrates.

Practical Action has a technical brief water-treatment-systems https://practicalaction.org/water-treatment-systems which gives a little bit of information about this.

For a general introduction to these issues the book Environmental Health Engineering in The Tropics: An Introductory Text by Sany Cairncross and Richard Feachem, published by Wiley is a good place to look.

For information on rainwater harvesting you can look at the book Rainwater Catchment Systems for Domestic Supply by John Gould and Erik Nissan Practical Action Publishing https://developmentbookshop.com/rainwater-catchment-systems-for-domestic-supply-pb