Below is a graphic of a rock bore well.
The water doesn't only enter the well from the bottom.
It enters anywhere from the bottom end of the casing to the bottom of the hole, due to seams between layers of rock, cracks and fissures in the layers of rock and any other geological formation that it can pass through.
Here is what the www.wellowner.org (Click Water Quality and then Coliform) says about Coliform bacteria contamination but it applies to salt water from a softener or road salting or any other contaminate.
If I have bacteria in my well, where do they come from?
Many experts in public health and water supply used to think that the subsurface was some kind of giant filter that trapped microorganisms before they could get to ground water, resulting in an effectively sterile water resource. However, we now know that many types of bacteria are native or adapted to saturated sediments and rock, and are indeed present in significant numbers in most water supply aquifers, even deep formations.
Given time and a route (soil and rock provide plenty of both), bacteria will migrate into and take up housekeeping in an aquifer. The environment is really rather nice- quiet, lots of surface area, often adequate carbon sources, and moderate temperatures with little environmental change.
Drillers and pump installers/servicers can also introduce microorganisms during their activities, but should not be considered the primary source of native microorganisms. There is no practical way at present to say for certain what is the source in any one well- maybe someday, but not yet. "Non-native" coliform bacteria or "protozoa" of potential health concern such as Giardia and Cryptosporidium are most likely introduced from the surface.
Here is a link to a graphic http://tylerwell-pump.com/default.aspx showing the Recharge Area (left edge up the hill) of a confined aquifer where any contaminate poured on or buried in the ground would contaminate the entire groundwater in a large area or region.
Rock Bore Well.