The water flows into, AND OUT OF wells all the time...
A well is nothing more than a deep spot on an underground stream, and if you pour the bleach in the well, it will be migrated out almost immediately and replaced with 'Raw' water.
It's much easier and more convent (not to mention using a bunch less 'Bleach' or whatever!) to have a large reserve tank, and when the tank is refilled from the well, add the bleach.
Since you know exactly were the pump comes on and when the pump goes off, you know how much water (within a few gallons) has been replaced in the tank, and most places with a 'Bad Well' have automatic cycling treatment tanks anyway...
When the tank gets full, it looks like a toilet tank float that administers a metered amount of disinfectant into the water... every time the tank is refilled...