The licence granted to Sellafield would allow the company to extract up to 77,077,224 gallons (350,400 cubic metres) of water a year until 2031.
The EA previously said it had considered all the potential impacts on the environment before giving permission.
Marianne Birkby, who submitted the challenge for LAND, said the group disagreed with the decision and would be looking to lodge an appeal.
It argued the environmental impacts of the licence had not been properly assessed and feared contaminated water would end up in the rivers Calder and Ehen.
“We feel we must challenge the Environment Agency’s continual rubberstamping of Sellafield’s wish lists,” Birkby said.
Sellafield said removing water from a construction site was standard practice when preparing land for a building project.
A spokesman said: “This water will not be discharged to the rivers Calder or Ehen. It is pumped to on-site storage tanks for testing prior to being discharged direct to sea.”
