Water in the backcountry and in water sources along the A.T. can be contaminated by microorganisms, including giardia lamblia and others that cause diarrhea or stomach problems. Waters may be clear, cold, and free-running and may look, smell, and taste good. In spite of all that, giardia and other waterborne parasites may still be present, and can cause debilitating illness. We recommend that you treat all water, using a filter or purifier or water-treatment tablets, or by boiling it.
They don't mention cryptosporidium, but they do go on to comment on the effectiveness of boiling, chemical tablets and filters against them.
For a through hike like th appalachian you wouldn't want to take the risk. That said, as has been pointed out previously, it shouldn't take anywhere near 4 hours with clear water that has no particulates.
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