I got my first filter about 15 years ago. For the 55 years prior to that I drank it like I found it. The body has it's own immune system and, if healthy, builds against repeated incursions by harmful pathogens. However, I lived and played in areas upstream from Industry and the masses of humans. ( Rule #1, drink upsteam from the herd.) As far as I know, all my bellyaches and other gastrointestinal malfunctions during that time was attributed to other than water borne critters. Anytime a person changes their excercise, diet, and sleeping patterns they can expect intestinal changes as well. Backpacker Mag did a study on filtration. It was an excellent read and one I wish I could find and reread. One of their studies involved setting up a question kiosk where people were coming off the AT. The questions were worded in such a manner that of the 200 plus people interviewed, after completing the questions 71 were convinced they had Ghiardia. But only 1 had been out past the 96 hour incubation period. All that being said, I now filter most everything just to be sure. But I still have a nice long sip of natural water when I run across a spring or fast moving small brook. But back to the original question, we are not talking drinking natural water while wandering the mountains. As a prepper concerned with water supplies during a long crisis, you can expect all types of contaminations, from petro chemicals to human waste and even the possibility of radiation in the waters. No one system is going to provide safe water in that environment. I don't have all the answers to that dilemna. I can only worry about what I may have to deal with in my area.
If you're talking about getting water free from chemical, bacteriological, or radioactive contamination, you're about going to have to go with reverse osmosis and/or distillation. This is probably not practical under many (most?) SHTF conditions. At some point, things are so fubared that nothing you can do will deal with the problem.
Like Grandpa, I didn't bother to treat drinking water from carefully selected sources for a long time...about 20 years of hiking on my own plus my entire childhood. I'll bet my dad has filtered or treated water less than a dozen times in a 70 year lifetime of hiking and never had a problem. It is known that there are some people who can ingest giardia and not get sick...since some of his hiking companions over the years have gotten sick from the same water sources he used, I suspect he is one of those lucky folks. That said, I started being more careful about it with my first pregnancy...I had a history that kept me from taking any avoidable risks. And I've continued to be cautious about the water I give to my kids. I've filtered everything for the last eight years or so. But I still wouldn't hesitate to drink questionable water, or give it to my kids, if it was a choice between unfiltered water and dehydration. The incubation for water borne illnesses is generally at least several days. You're likely to be out of the wilderness before you become ill, and that stuff can be treated. Death cannot be treated.
Reasons I prefer not to boil it: It uses a lot of fuel, which means more pack weight. It makes the water taste flat and, well, boiled. I don't want to wait for hot water to cool off again. That said, boiling certainly works. Just not my preferred method of dealing with water when there are a number of other very effective options. To each their own.
I grew up in Maryland as a kid and we had a well. When I graduated high school, my folks sold the house to some people from India of all places. They all got intestinal problems soon after moving in. We never had a problem because we were used to it. I still like to drink out of springs and small streams as long as I know nothing is upstream. In the early days we carried halozone tablets but rarely used them.
The problem is you don't know for sure what is upstream! "Beaver Fever" is caused by beaver feces. That stream could be running over a beaver dam! It is not worth the chance! A few years ago an" experienced" hiker was found dead in the Adirondacks 50 feet off the trail. He had written a note stating his mistake of not treating his water! HAPPY HIKING
I think the best method would be to boil the water. You could build some form of a filtration system out of birch bark, sand, charcoal, and grasses if the water isn't clear, but even then I would still boil it. The safest way is to let the water boil for twenty minutes. That should kill off any bacteria that may be present.
As a former hydrologist, I have problems with the UV method. I have sampled plenty of small streams and pools for water quality that are exposed to UV light 24 hours a day. Some of them are highly contaminated.
I've done a lot of backpacking in the Catskills and Adirondacks and rarely treat my water in the higher elevations. Springs of water coming from the side of the mountain and small upper mountain streams are generally potable. I spoke with a Catskill park ranger many years ago and he said he did the same thing and never had an issue in his 30 years on the job. As long as you pick your spots well, there is no issue. Lakes, lower valley rivers and streams I will always treat the water. In a long term survival situation as the OP mentioned, I would stick with a good filter or gallons of chlorine bleach, augmented by something like filtering water through cloth or the 3M scrubbies that can be bought in bulk in Home Depot, to remove the larger nasties. Of course it all depends on what you are trying to filter out of the water. The best filters, boiling, tablets, chlorine , etc. will not remove chemicals, pharmaceuticals etc.