Don't believe the folklore that "water from a spring is safe to drink"! Just because water comes from the ground via a spring (or well) doesn't mean it is clean nor safe to drink, particularly in karst (limestone) areas, where water reaches the aquifers and springs with little filtration (think of how quickly water can move down through a cave from the surface to the aquifer or spring.) The quality of water in a cave is dependent on what is upstream on the surface. Farms? Cattle? High mountain peaks with no habitation or farms? Mines? Housing developments and roads? Outhouses? Would you drink the water in the stream on the surface before it enters the cave?
Clean water emerging from the spring may have the benefit of soil and rock filtering after the cave stream sinks, whereas the water in the stream in the cave has likely had little if any filtration.
It's always best to err on the side of caution and treat and/or filter cave stream water before drinking. Even in remote areas giardia could be a present, just as in surface streams.
A couple of good publications that include a discussion of the particular issues with karst water and its quality:
"Living with Karst" by the American Geological Institute: http://www.agiweb.org/environment/publi ... /karst.pdf
"Living on Karst" by the Cave Consesrvancies of the Virginias: http://www.agiweb.org/environment/publi ... /karst.pdf