Water purification methods for waterborne pathogens and waterborne diseases, boiling works for these, chlorine maybe.

  Water in a compromised situation must be left on a rolling boil for no less than 1 minute, that's one minute after the water is actively boiling. At higher altitudes, such as when backpacking in the mountains,(>6,562 feet or 2000 meters) the water must boil for no less than 3 minutes. There are very few methods to sanitize contaminated water than boiling as it is 100% effective in removing Pathogens. Science Daily defines Pathogens here Link.

It's pretty, it's cold, it's clear and it's most likely contaminated
with Giardia, or some other Pathogen.

  Filtration may be used as a method to reduce most micro-organisms, but that depends on the size of the filter pores, the degree the water is contaminated, the particle size, and charge of the contaminant particle. I suggest conducting research and confiding in experts prior to the purchase of a filter. These filters employ a Chemical Disinfectant successful at riding the water of viruses, it's important to choose the correct ones. When using a chemical disinfectant water temperature, water clarity, PH, and many other factors must be taken into account when using a chemically treated filter.
  When boiling water is not possible a combination of filtration and chemicals are the most effective way to rid water of pathogens.
  UV lighting may be used to reduce micro-organisms and pathogens, however, the water must be filtered prior to exposure. In fact, the last stage in a "Reverse Osmosis" (Link) system employs Ultra-Violet lights. The water must be exposed to UV lights for the specific amount of time and power to reach a goal of maximum pathogen reduction.
  Chlorine when used in a salt solution which mixes oxidants, mostly chlorine, has little effect against Giardia but a high success rate eliminating bacteria and viruses. Giardia takes 2-3 weeks to show symptoms, a person will be long removed from the source when illness strikes, making associating the drinking water with the illness. Princeton has a really good paper on purifying water Link.
  Iodine can be used however, pregnant women, people suffering from Thyroid medical issues and those with a known sensitivity to iodine should avoid using it. Everyone else may use it for no more than a few weeks at a time.
  Boiling water to sanitize it is one part of the answer, personal hygiene being another. Bury feces at least 8 inches deep and 200+ feet from natural waterways. Wash hands a lot, prior to handling or eating food, and after using the facilities.
  Boiling is effective with the following:
  1)  Cryptosporidium: (Link) Commonly known as "Crypto", it's a disease caused by micro-parasites and able to live in the intestines of humans and animals, causing extreme diarrhea, vomiting, and cramps. The parasite finds it's way in this world by living in animal and human waste when it comes in contact with water, the drinking source is contaminated. Ways to remove it from water,
 *Boiling rapidly for no less than 1 minute, very effective in killing Crypto.
 *Filtration with an absolute or 1-micron filter has a very high success rate of removing this parasite. NSF standard 53 or 58 and rated "cyst removal/reduction filter". 
 *Iodine and Chlorine do a very limited job eradicating this micro-parasite, however.....
 *When using a 1 micron or finer filter along with Chlorine dioxide a very high effective rate in killing is realized.
  2)  Protozoa-Giardia, Giardia Lamblia, this is another disease from water contaminated with animal or human feces causing intestinal illnesses vomiting, cramps and diarrhea. It can be removed by:
 *Bring the water to a rolling boil and continue boiling for no less than 1 minute, this will kill Giardia.

This is a rolling boil, I use this photo a lot, it shows a good boil.

 *Filtration works with Giardia when a 1 micron or finer filter is used, the filter will be designated NSF standard 53 or 58 "cyst reduction/removal filter".
 *Iodine and Chlorine have low effectiveness in dealing with Giardia, although "Chlorine Dioxide" exhibits high success rates in killing this micro-parasite.
 *Filtration (1 micron or less) combined with chlorine dioxide is effective at eliminating this parasite.
  3)  Bacteria's, Campylobacter, Salmonella, Shigella, E. coli just to name a few, is also caused by water contaminated with human or animal feces.
*Bring the water to a rolling boil and continue boiling for no less than 1 minute, this will kill Bacteria.
 *Filtration works with Bacteria when a 1 micron or finer filter is used, the filter will be designated NSF standard 53 or 58 "cyst reduction/removal filter".
 *Iodine and Chlorine have low effectiveness in dealing with Giardia, although "Chlorine Dioxide" exhibits high success rates in killing this micro-parasite.
 *Filtration (1 micron or less) combined with chlorine dioxide is effective at eliminating Bacteria.
  4) Viruses, Enterovirus, Hepatitis A, Norovirus, Rotavirus are few viruses that infect water sources. It also causes the misery of gastrointestinal discomfort, diarrhea, vomiting, and cramps, also a source of Hepatitis and Meningitis. Again the water is infected by human or animal feces. More on human viruses in water Link.
 *Boiling is very effective, rapid boiling for no less than 1 minute, 3 minutes when above 6500 feet or 2000 meters
 *Filtration will not remove viruses.
 *Iodine and Chlorine treatments have a very high success rate in killing viruses. Chlorine or Chlorine Dioxide are both very accomplished at killing the viruses.
  This is merely Pathogens, Bacteria and Viruses, Chemicals, Detergents and Industrial waste are much harder to remove, some can never be removed from the water. In the California Delta, Mercury contamination is present, caused by Gold Mining. Not modern day Gold Miners, the '49ers would use Mercury to separate the gold from the base rock, then toss the rocks in a "slag pile". The piles grew to immense size, sitting in the mountains seemingly harmless. It has rained on the slag piles for over 150 years, the run-off carry's the slag downhill into creeks and tributaries. From there into the rivers where it settles on the bottom in the silt infecting the fish.
  Heavy metals are in the water, Mercury (above mentioned), Iron and Lead are a few, arsenic is another common contaminate. We will never know if all contaminants are eradicated without extensive testing of the water.
  Prior to determining if the water is worth even trying to purify we must ascertain where it originated. There is a big difference between purifying mountain creek water and cleaning up flood water, the former most likely treating for Giardia will suffice, the latter would take a super-fund cleanup in some cases.

We must assume all backcountry or open water should be boiled
prior to consumption.

  I have had Giardia twice, yep, once from a visit to Mexico, and the second from a backpacking trip in the Sierra's, it's not fun.
  It seems boiling is prudent no matter what the suspected contaminant may be, contamination from animal or human scat is capable of infecting almost any open water source. A combination boil, filtration, and chemical treatment may be our best course of action just to be safe. In historic era's fermentation was effective in killing many impurities present in their polluted water sources, which they were. Clean water has been a struggle since the beginning of mankind, dead animals, scat, minerals seeping from below ground and escaping gases have always been issues mankind has had to deal with. I live next to the river, I never thought of it before right now but the most pro-active task I could perform is to have water sample taken and tested. I will then be able to design my emergency water purification system to fit my particular situation. We all could benefit from surveying our possible source of water prior to an emergency event beginning.
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jacquesandkate    emergencykitsplus.com