people make a big hay out of untreated water being so dangerous to time-travelers or tourists but like, they're not at much more risk than the people who live there. even surface water can be a good bet with low enough population density and flow but if there's wells? heaps of folks draw their water directly from wells without treatment today, earth is an awfully good filter.
if something really bad is in the water the natives are being killed and then your story is just an epidemic/plague story (which are cool btw, but obviously authors don't want to do those for all historical/fantasy fiction)