Clostridium is a genus of soil bacteria including c. tetani (tetanus), c. dificil (opportunistic diarrhea in immune compromised patients), and c. botulina- not a common water contaminant problem. Giardia and cryptosporidia are the usual culprits- not bacteria, these are protozoa-critters-that are colon paarsites. Both are tough to kill, and both cause a relatively mild and usually self-limiting illness in folks with healthy immune systems. These are the bugs that will give you loose stools a week after exposure, and ones that you can seek cures for later on. Lots of folks who spend time in the woods are colonized with either or both of these, and have no symptoms.

Removing chemical contaminants, like pcb's is a little harder than inactivating the biologics.

Note to ponder: filtration removes the biological contaminants from the water: boiling and chlorine do not remove them, just kills them and leaves their tiny cadavers floating in your nalgene bottle-soup, of a sort.