It doesn't appear to be working at the moment. When I put the PET bottle or canteen in my hands and select "Use Pump" at a water well, the character goes through the animation of refilling the container, but no water is actually ever added to it. I tried waiting upwards of 3-4 minutes before giving up earlier today.
It should be noted that I was playing on a nearly full 1PP 75 player server. Upon attempting to fill the PET bottle while there were only 6 players on the server including myself, it filled perfectly and quickly on the first try. This appears to be an issue with server load.