As far as visible "crud" in the water, one possibility is to pre-filter it through a bandanna to strain that stuff out as you fill your container--I haven't personally tried this yet since my trips have been in places where it wasn't necessary, but it seems to be widely recommended. I also second the Crocs for stream crossings/camp shoes--they can be Crocs knockoffs, don't even have to be the "real thing". Much lighter than anything else you can carry for that purpose (other than nothing at all, which I don't recommend after one trip where I did that, had to cross a stream barefoot, and fell in!).