A Dwarf fell down a well
If his blood has terrible effects (e.g. if he was a vampire), AND your cistern is only one level deep, then the contaminants will become a problem. However, all contaminants (including things like demon ichor) are non-soluble and denser than water, so they will tend to sink to the bottom. Your dwarves use the well to get water from the top, so as long as the top is not the same as the bottom (i.e. the water in the cistern is at least 2 levels deep), having a contaminated well has absolutely no effect.