If a pump is pumping clean water, then it get flooded with contaminated water, it stops pumping. The pump will start working again on exit and reload or if you delete and rebuild the pump.
Here is another example of someone having this problem:
Also, I'm not sure if it might be related to this problem:
submerge a pump in clean water. make it pump. dump contaminated water into the pump. it will stop pumping until you reload the game.