Untreated sewage, agricultural run-off, saline water and fish pond effluent has made Jordan River unsafe for humans, said Gidon Bromberg of Friends of the Earth Middle East.
The reason, said Bromberg, was due to "ninety-eight per cent of the Jordan's fresh waters being diverted by Israel, Syria, and Jordan".
Friends of the Earth have called on "regional authorities to halt baptism in the lower Jordan River until water quality standards for tourism activities were met".
The Israeli site, known as Qasar al-Yahud, draws more than two million Christians each year. Thousands of them visit the holy site to be baptised.
Friends of the Earth argues that high levels of coliform bacteria from sewage in the river have made it unsafe for bathing. But water tests released last week suggest otherwise, Eli Dror of Israel's Nature and Parks Authority told Reuters.
"There's absolutely no problem with the quality of the water. People can come and baptise here as much as they want, I guarantee it," Dror said.
Tourism Minister Stas Misezhnikov said he was pleased that tourists would be able to continue visiting and using the site safely.
Israel's Tourism Ministry has invested millions of dollars recently to renovate the site, which is located in a closed military area near the West Bank city of Jericho.
It was in this river that two thousand years ago John the Baptist is believed to have baptised Jesus Christ and his followers.