Water on ships wasn't that clean to begin with. And things were made worse by people maybe not observing good hygiene. Think sharing cups, dipping those in the water, not washing their hands, etc. Imagine that, stored in a poorly sealed barrel on a ship with rats and other pests. Water was pretty bad on ships. People would get sick and weak on longer journeys (malnutrition, contaminated water, rotting food, etc.). A lot of their diseases would spread via water.

Beer had a head start on water because part of the process of making it involves boiling the water and the alcohol slows the growth of most of the pathogens. And it has some nutritional value.