I have had similar experiences here in Arizona and in particular in the Grand Canyon. If you get a heavy rain, the creeks will get really muddy. Most pre-filtering techniques like using a bandana or a coffee filter will only get part of the mud out. Even using a filter such as the MSR Sweetwater I use won't clean the water completely.

Pumping water to clean and purify it will quickly clog the filter so you need a filter that is field cleanable (this is why I use the MSR Sweetwater). Even with a field cleanable filter, you can only get so much water before the filter is rendered pretty much unusable.

When you are forced to get water in conditions like this, you don't have too many choices. You can look around for water pockets where clear water has collected and use that, you can boil your muddy water , you can filter as best you can with a bandana or its like and then add chemicals or you can pre-filter and then use a pump filter. Personally, I try to preserve the function of my pump filter. For this reason, I typically use the bandana and chemicals routine.

If you do a lot of desert hiking, this is something you have to deal with on occasion. Once you get used to it, muddy water can taste good, especially if you are thirsty. <img src="/forums/images/graemlins/wink.gif" alt="" /> I once had no choice but to pump water out of a water pocket that had a dead coyote floating in it. <img src="/forums/images/graemlins/tongue.gif" alt="" /> I survived but don't want a repeat unless necessary.