1) Label it 'contaminated well' and prevent the player from drinking or filling containers.
2) Don't label it and put up a message box telling the PC the water is contaminated and prevent the player from drinking or filling containers.
3) With or without a label, put up a message box telling the PC the well is contaminated and allow them to drink, but not fill containers.
4) With or without a label, put up a message box telling the PC the well is contaminated and allow them to drink, and/or fill containers, but make the containers permanently contaminated and create ill effects from drinking the water.
Examples would be:
Well Label: "Contaminated Well"
Message boxes:
"The water in the well looks and smells foul. You cannot drink from it or fill containers."
"The water in the well looks and smells foul. You cannot fill containers. Drink Anyway?" Yes/No (Yes causes some level of poison.)
"The water in the well looks and smells foul. If you fill containers with it, they will be spoiled. Fill Anyway?" Yes/No (bottle/jug/skin becomes tainted somehow. Not sure how this would work; probably best not to let them fill containers) "Drink Anyway?" Yes/No (result same as above)
This way, if the player is about to die of thirst, they can still choose to drink the contaminated well water, which will restore their health first, but then poison them. Or it will only partially restore their health.