For a sense of scale, however, 50 gallons/minute works out to 72,000 gallons per day, whereas an Olympic-size swimming pool contains ~660,000 gallons of water.
It would take slightly more than 9 days to fill just a large swimming pool, which means that as long as the water is able to flow out into the local river system, you should be just fine unless you're adding large numbers of these fountains, in which case there's a point at which you could cause flooding downstream and invite declarations of war from very upset kingdoms. If all you want to do is have a purified source of water for drinking, with any excess then being utilized by your public bathhouses before being used to flush out your sewer system, you should be all good, but stick to the Kamelands, which are hilly enough to support natural drainage.
Personally, I feel that there is a lot that is missing from the rules, even the improved set from Ultimate Campaign. For example, there's plenty of references to sieges, but no actual rules, so it's not like there's some stat that you could add a bonus to for resisting a siege better on account of unlimited freshwater.
What I would go with, without adding all new rules and other complications, is that it has no inherent effects, but provides water for up to X buildings that require water to function (such as a brewery or public bath), and that you need to either be adjacent to a river/lake, have an aqueduct/canal, or one of these fountains to build those buildings.