There's a lot of misunderstandings about water treatment. Unfortunately if you get it wrong the results can be downright sh***y, if you know what we mean. Even in wilderness that seems pristine you can get baddies lurking in the water. Northern Saskatchewan has areas where Giardia (Beaver Fever) and Cryptosporidium (another protozoa that forms cysts) are present. They are transmitted through animal and human feces and can live for months in cold water, and all it takes is a few cysts to bring you down.
No matter which treatment method you use, the cleaner the water is, the better. Particulate can clog up your filter, reduce chemical effectiveness or interfere with UV light. If the water is murky either pre-filter it through a bandana or let it sit until the sediment settles, then siphon the clearer water off the top.
There are two main ways to treat water:
Filtration physically removes particles from the water by forcing it through some sort of filter. Since some bacteria can be as small as 0.2 microns, you need to make sure your filter can catch these little buggers. (Just to give you an idea, the period at the end of this sentence is about 500 microns.) Effective filters remove protozoan cysts and bacteria, but viruses are too tiny to get caught.
Purification takes nothing out of the water but kills the bad stuff through boiling, chemical treatment or UV light. It gets rid of protozoan cysts, bacteria, and viruses. If you are traveling off continent you will need to be prepared to purify your water.
It is always a good idea to take a backup method for water treatment. If you have a filter, bring along some water purification tablets as well. As a last resort - say your ceramic filter shattered and your tablets went up the tree with a squirrel - you can boil your water to make sure it is safe to drink.
Pros and Cons
Boiling is the most effective way to kill pathogens in the water. However it takes time and fuel, nobody likes drinking warm water, and boiling gives your water a really bleh taste.
Filters are great in that they make the water cleaner. The taste of the water is unaffected. The downsides are that they don't remove viruses, the filters need maintenance and may break, and hand pumping is a pain (gravity feed filters take care of this problem however).
Chemicals (there are many chemical treatment products, but they are either iodine based or chlorine based) kill almost everything in the water. They add a yuck flavour however, so you may need to bring along some Kool Aid crystals to disguise the taste. They also don't get rid of particulate matter, so you may be picking duckweed out of your teeth.
UV light purifiers kill everything. They are also very quick to use and do not alter the taste of the water. You may still get duckweed in your teeth, and you do need to make sure you have enough batteries with you, but the lamps last for up to 8000L of water and don't use much battery juice.
There are a lot of different ways you can go with water treatment - just make sure you consider where you are traveling and what features are important to you.