I have had good results using alum (used for making pickles, find it in the spice section of most gorcery stores) to settle water on the San Juan. If you get the chemistry right you can get a 5 gal. bucket to settle to clear in about 15 minutes. Our group likes to bring potable water for drinking and a small filter for backup. We use the settled water treated with bleach for dishwashing and bathing.
There is a LOT of silt in the water, untreated it would clog a water filter in no time.
Here are detailed instructions for using alum....
Water Treatment for Rafters
I did not need to adjust the PH for the San Juan, just added the alum solution,(about 1/2 tsp per 5 gal bucket if I recall.) The ratio has to be just right, so experiment a bit. Disolve the alum in 8oz of water first, doesn't work well if you just add the powder directly.
Without alum the water had to sit at least overnight and didn't come out as nearly as clear. Note: critters like to crawl into the buckets overnight. Any uncovered buckets had a floating dead mouse by morning, so bring some lids! If your filter clogs or fails during the trip you better have a backup plan, I wouldn't want to drink water out of the San Juan untreated.