Bacteria which are found in wells can be divided into two broad classes: disease causing bacteria - of which Escherichia coli (usually known as E. Coli) is the most famous example - and nuisance bacteria, which are responsible primarily for aesthetic problems.
The presence of disease causing bacteria can be determined by water sampling. Most local health units provide free testing for E.Coli and total coliform. Other accredited labs will provide testing for E.Coli and total coliform, as well as many other kinds of bacteria including fecal coliform and fecal streptococci, and nuisance bacteria.
Shocking the well with chlorine provides immediate but potentially short-lived relief from problems with this type of bacteria. The installation of an ultra violet disinfection system offers more permanent protection.