After some research, I found information on how to remove the bacteria from a private well. This essay explains how to chlorinate your well. There are several ways that bacteria can get into a well. Often, after a flood many wells in the area become contaminated with bacteria. This can happen if the wellhead gets submerged, allowing dirty water to leak down into the well.
Shallow wells are more likely to become contaminated than deep wells.
The types of bacteria that usually contaminate wells are coliform and E. coli bacteria. These often come from animal waste. This type of bacteria can cause stomach discomfort and diarrhea. E. coli bacteria can cause serious illness and even death. Private wells should be checked periodically and especially after flood conditions.