The next time you’re thirsty, you might want to consider buying a bottle of water instead of sipping from a water fountain. It seems that these public drinking fountains do sometimes harbor unwanted germs and pathogens. 
Concern over the safety of public drinking fountains was once greater than it is now. People who lived through the polio epidemic of the 1950’s, for example, tend to be more fearful of slurping from a public fountain. The disease was spread through feces, and swallowing just a tiny amount could kill you. Polio tended to strike children more often than adults, and so many parents understandably pulled their parched youngsters away from drinking fountains when they were out and about.
The health risks associated with water fountains come mostly from the people that come in contact with them, not from the water that flows through them. Fountains are constantly being rinsed, so even if children put their mouths right on them, the water is still fairly clean. But sometimes people spit in the fountains before drinking out of them, or people let their dogs drink from fountains intended for humans, and that’s where the germs come from. (Note: few germs adapted to dogs are easily transmitted to humans.)
Most contamination comes from the rims and handles of water fountains. Just like doorknobs, subway poles, computer keyboards, or anything else that multiple people touch, they can harbor dozens of bacteria or viruses transmitted via feces, mucus, or coughs.
That’s not to say that there is no danger posed by the drinking water in public fountains. According to a recent CDC report on waterborne diseases in drinking water, public health officials from 14 states reported 32 outbreaks linked to drinking water between 2011 and 2012. These outbreaks resulted in hundreds of illnesses and 14 deaths. Most of the cases were associated with Legionnaire’s disease; the remaining cases were caused by norovirus, E. coli, Shigella, giardia, or other pathogens.
Most of the water in the cases cited by the CDC was from camps fed by springs and lakes, or in small communities with wells near broken septic systems. In city buildings, the outbreaks were blamed on shoddy plumbing. City water flowed through filters that removed chlorine, which had themselves become contaminated with bacteria.
Legionnaire’s disease is back in the spotlight in the U.S. due to outbreaks in New York, California, and Illinois in recent years. The CDC has said that even though the number of outbreaks this year has fallen within the normal range, the number of cases per outbreak has been higher than normal and that cases are more common in late summer and fall. 
The disease is caused by the Legionella bacteria and can cause life-threatening cases of pneumonia. The bacteria grows in warm water and is often spread through air condition cooling units, fountains, hot tubs, or large plumbing systems. It must be inhaled in order to cause infection. The illness has a two-week incubation period. 
Still, Legionnaire’s is more likely to be found in decorative fountains than drinking ones. In 2010, a “wall of water” feature in a Wisconsin hospital lobby infected 8 patients with the disease. The bacteria were found growing in the foam material that was supporting the fountain’s decorative rocks.
 ABC News