This post may contain affiliate links.

Desert Water Purification: Challenges and Solutions

Desert Water Purification
Purifying water in the desert can be a unique challenge. Often, it’s hard to even find any water to begin with, and when you finally do, it’s opaque with silt or full of swaying algae or tiny worms. Much of it is frankly unappealing. In this article, I will discuss pathogens, purification methods, challenges unique to desert environments, and solutions. Most of what I cover saying pertains to the dirty, filthy, sandy, silty, muddy water sources that transect the Colorado Plateau, including Grand-Staircase Escalante National Monument, Bear’s Ears National Monument, Canyonlands National Park, The San Rafael Swell, and Grand Canyon National Park. Although the lessons learned can also apply to the Sonoran Desert, the Mojave Desert, and the Great Basin Desert, as well.

Desert water can be silty, muddy, or buggy.
Desert water can be silty, muddy, or buggy.

Water Purification Methods

Water purification involves the removable or neutralization of protozoa, bacteria, and viruses, whereas water filtering just involves removing or neutralizing protozoa and bacteria. Some water purifiers can do this by filtration, like the MSR Guardian, because they have a filter pore size that is small enough to remove virus particles. In the desert, multiple stages of filtration, followed by purification may be required as we discuss further below.

There are four main methods of purifying water.

  • Boiling
  • Filtration (with a filter rated by the EPA for purification and not just filtering)
  • Chemicals
  • Ultraviolet Light

Boiling is usually a little too time-consuming and fuel-consuming to be practical, so I won’t discuss it much here other than to say it works but I consider it a last resort. Filtration works well in desert environments with clear water, as well as silty water, although your filter will last longer and require less backflushing if you let the silt settle out before filtering. Chemical purification with chlorine dioxide is most effective with clear water and is a good secondary method to use after water has been filtered. Ultraviolet light relies on clear water but depends on batteries, which I feel, increases the risk of possible failure in a desert environment.

This desert water is clear but has little worms in it.
This desert water is clear but has little worms in it. Yuk.

Pathogens and Impurities

There are various biological and chemical impurities in desert water that we want to be able to remove or neutralize.

a. Protozoa and bacteria can be transferred to you through human or animal fecal matter in the water. These can be removed by regular water filters, purifier grade water filters, or neutralized by boiling, UV light, or chemical purification.

  • Protozoa, including cryptosporidium, giardia.
  • Bacteria, including E. coli and salmonella.

b. Viruses that are harmful to humans are transferred primarily by the fecal matter of other humans, including other backcountry visitors and upstream wastewater plants. They can be removed by purifier grade water filters, or neutralized by boiling, UV light, or chemical purification.

  • Viruses, including norovirus, norwalk, rotavirus, hepatitis A.

c. Heavy metals, pesticides, fertilizer, and mine tailings as a result of upstream industrial or agricultural activities. These are much more difficult to remove safely and in their entirety. The best way to avoid them is usually to plan your route to bypass areas where they are present.

  • Heavy metals including lead, chromium, arsenic.
  • Chemicals including chlorine, benzene, chloroform.
  • Other contaminants including herbicides, pesticides, and fertilizer.
Floating by a dead cow in Utah's canyon country
Floating by a dead cow in Utah’s canyon country

Additional Water Purification Challenges

These are the biggest additional challenges to finding and purifying water in the desert.

  • No water to purify
  • Silty water
  • Seasonal changes making sources unreliable
  • Climate change making sources unreliable
  • Freezing temps

No water to purify

Hopefully, your trip planning removes a lack of water from the equation, but it is a very real consideration in the desert. I would recommend consulting as many different sources as possible to verify the reliability of any water source you plan to use. Check satellite imagery, consult recent trip reports, look for springs marked on USGS maps, and call the Forest Service, Bureau of Land Management (BLM), or National Park Service (NPS) ranger station that manages the area where you will be backpacking and ask about the latest water reports. Call the locals. Check the region’s Snotel sites to gain a greater understanding of general water availability determined by a good or bad snow year. Check USGS water gages in the area where you will be backpacking. Even if you don’t plan on purifying water from one of these streams, their proximity to your backpacking destination may give you a good idea of how much water is available in the area. Cross-check your findings with the water sources noted in Michael Kelsey’s Non-Technical Canyon Hiking Guide to the Colorado Plateau. He notes all water sources he encounters and usually notes the time of year they were available.

Many rivers in canyon country are completely opaque.
Many rivers in canyon country are completely brown and opaque.

Silty Water

The exposed geology of the desert southwest is one of the things that makes it so striking, but it’s also the reason the water is often so silty. Rivers like the Colorado River, the Green, the Dirty Devil, and the San Rafael are completely opaque with silt. The best thing to do with silty water is to settle it in order to separate the silt from the water, although I try to plan trips around clean water sources so settling isn’t necessary. This isn’t always possible, however.

To settle water, you should carry a bucket like the Sea To Summit Folding Bucket – 10L. It costs about $30 and weighs 2.8 oz and is very worth the weight and cost. Fill it with opaque, greenish-brown, turbid river water at night and let it settle until morning. Use a cup or pot to carefully scoop clear water from the top trying not to disturb the layer of silt at the bottom. Settling turbid water is a necessary step before you can use any of the purification methods noted above.

Silty water should be settled in a folding bucket
Silty water should be settled in a folding bucket

Seasonal changes making sources unreliable

The Colorado Plateau gets most of its water from snowmelt, so there is more water available in winter and spring, and less available in summer and fall. The only time this isn’t true is when the monsoons come between June and November. While they usually result in flash floods, they also often fill up potholes and tanks with tasty, clear rainwater. If you embark on a trip right after a good monsoon you may have good water sources that are not labeled on maps.

Climate change making sources unreliable

Climate change has made the southwest desert hotter, which means that precipitation that would normally fall as snow in the winter is falling as rain. Snow acts as a natural reservoir, slowly dispersing water as the season warms. Springs and streams reliant on snowmelt are going to sometimes flow earlier in the season and become depleted earlier in the summer. Checking the Snotel sites and USGS river gages can help you plan around these uncertainties from year to year.

It can freeze at night in the desert and wreck your water filter.
It can freeze at night in the desert and wreck your water filter.

Freezing Temperatures

Water is most available in the Colorado Plateau in the winter and spring which means you could be out backpacking in freezing temps. Freezing will damage most filter-based purifiers, so they must be kept warm. Some people opt for the reliability of chemical tablets in such circumstances although they require longer reaction times to work in colder water.

Comparison of Purification Methods for Desert Use


I’ve tried a variety of water filters in the desert including pump-style filters, gravity filters, and bottle-based filters. These aren’t true water purifiers (according to the strict EPA definition) because they don’t remove viruses, but they can act as the first stage in a multi-step process, followed by chemical or ultraviolet light purification to neutralize viruses.

Many pump filters, including the Katadyn Hiker Pro have a pre-filter at the end of the intake hose to remove larger contaminants (down to 150 microns) before they reach the filter element. You’ll still want to settle your water before filtering it to avoid clogging the main filter element prematurely though. The problem with a pump filter like the Hike Pro is that will get harder to pump as contaminants are trapped inside. While you can field-clean the exterior of the filter you can’t backflush it to make it flow much faster. The MSR Guardian is the only exception to this that I know of because it backflushes its filter constantly (see Philip’s MSR Guardian review), but it is a really expensive water purifier.

Desert water will kill your filter quickly if you don't have the option of settling.
Desert water will kill your filter quickly if you don’t have the option of settling.

Based on my experience, I’ve found that gravity filters like the Platypus GravityWorks 4.0L Water Filter System are a better option than pump filters in the desert (see Philip’s Platypus GravityWorks review.) First, they are lighter, which is important when you’re likely going to be carrying a lot of water in your pack. Second, they can be easily back-flushed. For example, the GravityWorks reservoir configuration can be simply flipped upside down to push sediment back into the dirty bag. The silt will eventually kill your gravity filter too, but you can switch to a less expensive filter instead like the dual-threaded Sawyer Mini or a HydroBlu Versa Flow to save money,

Bottle filters are a third option, but they can only process a small amount of water at a time. In the desert, it’s worth processing a large quantity at once and carrying it with you, so having a system that lets you do this quickly and efficiently is important,

Chemical Water Purification

Chlorine dioxide is the best chemical treatment for desert use and very effective against all pathogens. It also has no taste and is used widely to treat water for municipal use. I always carry Aquimira’s chlorine dioxide liquid treatment solution in my pack, although it’s also available in tablet form. Chemical treatments such as iodine and chlorine bleach are not as effective: iodine is only moderately effective in killing giardia lamblia, according to the CDC, and ineffective against cryptosporidium. Chlorine bleach is also ineffective against cryptosporidium.

The treatment time for Aquamira is 15 minutes for clear water to kill bacteria and viruses, including Giardia and Norovirus, or 30 minutes if your water is very cold because it takes the chemical reaction longer to occur. If Cryptosporidium is present or a concern, the treatment time is 4 hours. However, you can reduce the treatment time to 1 hour, if you double the number of Aquamira drops you add to the water you wish to treat.

Aqua Mira Water Purification Drops
Aquamira Water Purification Drops

I try to plan my routes well so that I’m filtering mostly from very clear water sources. This way I can use Aquamira for the majority of my purification. If you don’t process your water through a filter first, I’d recommend straining it through a coffee filter or settling it which I discussed above before adding Aquamira too it. Aquamira can freeze, so it might be a good idea to carry some Aquamira Water Purification Tablets instead (or Katadyn Micropur tablets which are easier to find) or to sleep with your Aquamira liquid to keep it warm.

Purification with Ultraviolet Light

Ultraviolet light from a Steripen neutralizes all the same pathogens as filters and chemical treatments (by damaging their DNA so they can’t reproduce inside you). Steripens work best with clear water, but longer treatment times are required for turbid, murky, or cloudy water.   I have never used one, however, because I don’t like the idea of relying on batteries for something as critical as water purification. Mechanical and/or chemical treatments give me more peace of mind in the desert. Note: Katadyn also sells a Steripen with a prefilter to help clarify murky water before treatment.

If you can find potholes to purify (filled by rain or flood), it will be some of the clearest, tastiest water in the desert
If you can find potholes to purify (filled by rain or flood), it will be some of the clearest and  tastiest water in the desert


The best way to assure water availability when backpacking in the desert is to know the environment well. Check and cross-check the planning resources referenced but don’t rely solely on any of them alone. Bring a settling bucket or container. Build some redundancy into your hydration water purification system. Carry Aquamira and a Gravity filter or a Pump purifier, for example. Try to plan trips according to reliable, clean water sources, while also being prepared to drink from suboptimal sources like big rivers and cow ponds.

SectionHiker is reader-supported. We only make money if you purchase a product through our affiliate links. Help us continue to test and write unsponsored and independent gear reviews, beginner FAQs, and free hiking guides.


  1. Over the last half century and more, I’ve done many backpacking and river trips in the Big Bend/Rio Grande area and I can identify with much of what you wrote.

    When I didn’t have time to let silty river water settle, I’d have to back flush a Sawyer Mini after every half gallon. I rigged a gravity filter system with that. There no way I wanted to squeeze water through a continuously clogging filter.

    When collecting water from slimy algae ridden water holes, if the hole is deep enough, I hold my collection bottle with the opening down to get past the surface glop and then turn it sideways under water to fill with the clearer water between the surface and the easily stirred up silty bottom. Even after that, I’ve also used a Coleman fuel filter with fine mesh screen as a pre filter.

    My father managed oil exploration crews all over the world, from the oceans, to the Arctic, jungles, and deserts. He’s told about collecting river water for a camp somewhere in Africa just prior to a dead camel floating by.

    There was also the time the water in his hotel along the Amazon, although soft, was yellow, smelled bad and tasted funny when he brushed his teeth. He asked the hotel manager about it and the manager took him outside, pointed up and asked,
    “You notice the parapet on the roof?”
    “Oh yeah, you collect rain water. No wonder it’s soft. But why does it smell and taste so bad?”
    “You see the buzzards on the roof?”
    “Yes, I see them.”
    “Notice, the beaks are out, the tails are in!”

    Some days, you wish you had a Sawyer!

    • Love these anecdotes! Thanks for sharing. I also have rigged a gravity system with the Sawyer Squeeze and a 3L Platypus. Seems to be the cheapest, most reliable gravity option for me. ~$35 for replacement cartridges. And I backflush it often, as well.

  2. During my traverse of Southern Utah I had very good success using alum as a settling agent when the crude water was silty. A saturated solution of alum, about 1 oz per fl oz of water, in a dropper bottle is all you need. You add 5 drops of this solution to the water and wait 15 min. Then you decant the top 80% through a filter, a 1 micron sump pump sock in my case, into another container and you have perfectly clear water for sterilization by whatever method. Even water from the Dirty Devil which looked like cement water became perfectly clear.

    I do not claim to have invented this. I am merely spreading the word.

    • Your reply prompted me to look up “Treating Water with Alum”. There’s some really practical information on this. Thank you for bringing it to my attention. It will go into my toolbox for use on trips in areas with turbid water.

    • I’ve used this once and it did work. Thanks for mentioning!

  3. I’ve filtered and purified water several different ways. I’ve slept with my filter to prevent freezing, but I’ve also had my filter in my pack during freezing temps. I was never quite sure if my first Sawyer Mini didn’t freeze some internally while inside my pack, so I replaced it as a measure of caution. Is there a way to determine if a filter element has been compromised?

  4. Walking the PCT desert section and all the rest to Yosemite we used bleach/Clorox in a Murine bottle(dump the Murine). Two(2) drops /Liter running water/4 drops/Liter still water.

    Wait 15 minutes and drink. We never used a filter.
    Most restaurants have bleach in the kitchen and would refill us as needed.

    No one got any sickness period and the coffee was great.

    Check the Clorox page for purification details if you don’t believe me.


  5. Are the threads on the HydroBlu Versa Flow compatible with Platypus bottles?

  6. 31 years of Desert Backpacking in Southern California, Arizona, New Mexico, and Baja Mexico. I only use or used the First Need Deluxe Water Purifier. Never had a problem. I still use it now that I escaped from California an live in the central south.. With only Filter Changes I have been using the same Pump Unit now for over 20 years.. I’ve never had a stomach problem or caught any kind of intestinal bug… We collected most of our water from Desert Potholes many of which we had to follow the Bees to locate underneath some house size Granite Boulders to find some pothole with algae and some kind of swimming critters in… The First Needs prefilter took care of most of the problems and we just had to wipe off the Algae from that… I’m allergic to Iodine containing products after some 30 years of using them so the First Need is my one an only water treatment. By backup is a Sawyer Survival Straw but I have never had to carry it..

    • I think General Ecology’s First Need filter is hugely underrated. They have decades of history in water filtration, but lack the marketing prowess of a company like MSR. I’ve handled the MSR Guardian, which has great features for sure, but the First Need still has an edge on being able to filter out chemical pollutants in addition to dirt, bacteria and viruses. Flow rate is still quite high, and the construction is just as durable with fewer fiddly pieces to break. One of the best kept secrets in the backpacking world!

Leave a Reply

Your email address will not be published. Required fields are marked *

Captcha loading...