Ships carried literal tons of fresh water. I'm not sure the details of treatment or how it was provisioned—provisioning beer was such a massive logistical task we have mountains of records, but we have a paucity of corresponding records for water—but we have sufficient records of what happens when that fresh water disappears or becomes tainted to know it was of paramount importance.

Keeping water fresh is not quite as difficult as you might think. For one thing, wood has naturally antibacterial properties; it can be trivially sealed with pitch and tar (which also has antibacterial properties), and it just takes one quartermaster to babysit it.

If anything, beer is a way of preserving calories and boosting morale. The fact that drinking a gallon of it translates roughly to drinking 97% of a gallon of water and does end up being quite hydrating just doesn't imply that people didn't also drink water sans beer.