It depends on how you interpret the question.
As the author of the article you linked points out, when Medieval humans were offered a choice of dirty or fetid water or an alcoholic beverage (beer, mead, or wine) they would choose the booze. The article abundantly documents this fact.
However, when water that had no detectable contamination was available, or when one could not afford the cost of prepared beverages, water was consumed without fear.
I don't know if the the author is aware that filtering water through a honey-skep or adding wine or vinegar (aka spoiled wine) is a partial disinfectant, since he doesn't mention this. It's unlikely that most Medieval people knew it either, although it was known to some in antiquity.
Anyway, an article well worth reading if you are interested in the European Medieval period. Thanks Rob!