Giardia is a waterborne pathogen, a microbial parasite similar to cryptosporidium that infests the intestine causing severe cramping and diarrhea. It is passed on in a variety of ways but the primary threat to hikers is from drinking water or eating food that has been contaminated by infected fecal matter. Symptoms appear in three to 25 days of contact. It is a resilient pathogen which can survive for a long time and is resistant to chlorine disinfectants.
There has not been much research done but there have been two studies in the last twenty years that a more important factor in staying healthy while hiking is keeping good hygiene habits. The studies asserted that unwashed hands caused these symptoms much more often than waterborne parasites.
One research team found that the more remote and pristine the area, the less likely it was that there would be microbial contaminants in the water. That does not mean that it is not a hazard but rather one of many and hikers should always be careful to wash their hands and filter their water.