Filters make up the biggest chunk of your water treatment options. By definition, filters physically strain out offending critters larger than a given size. Some filters remove, or filter out, protozoans and bacteria, and there are filters that "purify," which means they remove viruses, too. Which type you choose depends on the degree of risk you're willing to take. Obviously, purifiers are the safer way to go because they strain out the hard-to-get viruses. But purifiers cost more, and they tend to clog more quickly than nonpurifiers. All filtering devices clog eventually, some sooner than others. Since a plugged-up filter does you about as much good as a tent without a roof, this is an important factor to consider when shopping.
For many years now, boiling has been the most foolproof way to make your water safe because no micro-cootie, no matter how tenacious, can survive a rolling boil. Experts disagree on how long water needs to boil in order to be safe for drinking. Some say just reaching boiling point (212°F) is sufficient. Other say you must sustain a rolling boil for 3 minutes.
Boiling is foolproof in the sense that you don't have to rely on any mechanism other than your ability to start your stove or to make a fire. While boiling does have drawbacks, like using up fuel and time, it's the way to go for your cooking water. In other words there's no need to filter or chemically disinfect water that you're going to use to cook rice. Just dip your pot in the stream, set it on the stove, and bring it to a boil.
One other option for treating your water: iodine, which comes in tablet, crystal, and liquid forms. For years iodine has been the most efficient way for backpackers to treat water because it's lightweight, cheap, and as easy as dropping a sugar cube into a cup of coffee. Iodine has its downside, however. First, if you're dealing with murky, foul-tasting water, iodine does nothing to make it more appealing. In fact it makes it taste even worse. Second, and more importantly, experts recently have discovered that iodine doesn't kill Cryptosporidium, a protozoan that's becoming increasingly common in North American backcountry water.
The last option is liquid drops, which use chlorine dioxide to disinfect water. The two manufacturers who make the drops, McNett and Aqua-Lung, claim that when mixed correctly, they take care of Giardia and Crypto.