There's a lot of confusion on how to make backcountry water safe for drinking, so here's some up-to-date information. Remember, the appearance of wilderness water has no bearing on how safe it is. Even a crystal-clear mountain stream can be contaminated with disease-causing organisms.
Except in the rare case of a spring that is poisonous due to chemical contaminants, what we're worried about are pathogens- bacteria, viruses, and protozoa. While most waterborne diseases in the United States are caused by bacteria and protozoa, viral diseases such as hepatitis are occasionally encountered. Outside the U.S., viral contamination of water is much more common. There are two common disease-causing protozoa which have been found in backcountry water, giardia and cryptosporidium.
The most common health effects from drinking contaminated water are digestive system disorders such as cramps, vomiting, and diarrhea. These can be mild or totally debilitating requiring a helicopter evacuation. In any case your wilderness trip will probably be ruined, so it's a no-brainer to purify all wilderness water sources, including springs. A possible exception is melted clean snow.
There are three basic methods of purifying water- boiling, filtering, and treatment with chemicals.
Without a doubt, boiling water is the most effective method of purifying it. Bringing water to a rolling boil for one minute kills bacteria, viruses, and protozoa. Unfortunately it uses time and fuel, and leaves you with hot, flat-tasting water. You can pour boiled water back and forth between clean containers to aerate it and restore the taste.
Filters and filter-based purifiers are popular, though most are heavy, slow, and bulky. Most filters use hand-operated pumps to force water through the filter elements. Some systems are gravity-fed and can treat large amounts of water fairly quickly. These tend to be even heavier and are used by large expeditions and river trips.
A plain filter is very effective against protozoa, moderately effective against bacteria, but not effective against viruses. Some filters have an active charcoal element which removes chemicals that cause bad tastes and odors. A purifying filter adds an active halogen element (usually iodine) that kills bacteria and viruses.
Chemical treatments include iodine and chlorine dioxide tablets and chlorine in the form of household bleach. Chemical treatments are lightweight and compact, but their effectiveness varies with the temperature and amount of organic contaminants such as plant matter.
Iodine and chlorine are effective against bacteria and viruses, and moderately effective against giardia but not cryptosporidium. Chlorine dioxide is effective against bacteria, viruses, and giardia and is moderately effective against cryptosporidium.
For wilderness travel in the United States, chlorine dioxide tablets offer the best combination of light weight and effectiveness. For travel in parts of the world where water-borne diseases are common, a purifying filter system is the most effective system. Or, you can use a plain filter system and then treat the filter water with iodine or chlorine dioxide.
Always follow the manufacturer's instructions and recommendations, especially in regard to doses and wait times.
See the Centers for Disease Control Web page on backcountry water purification for more information.
http://www.cdc.gov/healthywater/drinking/travel/backcountry_water_treatment.html
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