Water that is deep underground, such as that from an aquifer, is more likely to be pure and of drinking water quality than water that is just below the surface (usually referred to as "groundwater"). This relative purity has not changed despite the use of pesticides or fracking or the other horrible things that other perhaps well-meaning responders with political agendas would have you believe so you can join their bandwagon. A group that does excellent work, Engineers without Borders, has dug wells in Africa to supply good quality water to people there who were previously burdened with horrific disease rates from poor water quality. The villagers do not need to boil the well water (or treat it in any way) to make it safe to drink but they draw from the well as they need water and do not attempt to store it in tanks.
What makes water unsafe to drink in Africa and other places is poor (yet completely natural and often pesticide and fracking-chemicals free) sanitation. This lack of sanitation results in water contaminated with microorganisms that cause diseases with symptoms of diarrhea or worse. Chlorine or chloramines in low quantities are added to water in developed countries to prevent the growth of these microorganisms, not to create poor health among unsuspecting civilians. People who store large quantities of pure water in tanks for their own use risk the growth of microorganisms if the turnover of water is not sufficient (so be careful Mr "Snowy Whatever" when you come back from a month away from home - be aware that the pure water in your tank is not then as likely to be safe to drink).
In brief, it is rare that chemicals cause water to be unsafe to drink. It is common that microorganisms contaminate water through completely natural processes.