Most of the water filters carried by backpackers and long distance hikers cannot remove organisms smaller than 3 microns in size. While protozoa such as Giardia (shown below) and Cryptosporidium are about 5 microns in size, water filters miss bacteria such as Cholera, E. Coli, and Salmonella (0.2 – 0.5 microns) and viruses such as Hepatitis A, rotovirus and Norwalk virus (.004 microns).
The safe solution is to always use a water purifier such as Chlorine Dioxide after you filter your water. However, like filters these chemical additives have limitations that you need to know about in order to prevent getting sick. All chemical additives have difficulty purifying water that contains sediment because the particles suspended in the water interfere with the chemical reaction. Therefore, filtering to remove the sediment or letting the water sit overnight so the particles can settle before purification is recommended. In addition, cold temperature slows the purification process if your water is below 60 degrees F. As a general rule of thumb, you should double the recommended contact time for every 20 degrees F below 60 degrees F.
P.S. I went whitewater kayaking in October, 2007 with an old friend and kayak mentor who is in charge of the chemical engineering unit responsible for certifying water purification technologies for the entire U.S. Army. He was adamant that the combination of water filtration and purification are needed for backcountry travel in the eastern US, for the reasons I cite above. He’s also a sectionhiker.