Environmental threats:

In attempt to control drug production the US has undertaken projects to spray the coca plants "with chemicals that not only destroy the coca plant but contaminate the groundwater and legal susistence crops."
http://www.lightparty.com/Misc/COCALEAF.html

Mining: (info from http://www.natural-resources.org/minerals/docs/oecd/Global%20Forum%20FDI%20&%20Mining%202002/Relevance%20of%20OECD%20Guidelines%20for%20Multinational%20Enterprises%20to%20Mining%20Sector%20and%20Promotion%20of%20SD.pdf)

Acid mine dragains (or AMD) is a solution originating at a mine site and carried off in rain or surface water. It is deposited in all nearby watersources including the groundwater and is often extremely acidic with high concentrations of toxic metals.

Groundwater is depleted (along with surface water)

"Heap leaching using cyanide or sulphuric acid poinsons rivers, streams, and groundwater and kills fish and wildlife."

Tailings, the ground waste form the mined rock after the target minerals have been removed, can leak from where they are stored behind and earth filled damn polluting the surrounding water and soil.

The effects of deforrestation:

Scientist commonly expect the neutrient concentration of riverwater to decrease with heavy rains because the source of these neutrients is the ground water. In the Amazon Basin, this was not the case. The found that concentrations actually increased. There is no agreement upon the cause, but theories include an increase in rainfall washes the neutrients out of the soil into the river. This is OK while there are trees present, but deforistation causes them to be leached out faster than the new sediment deposits them.